Sample preparation

PDBx/mmCIF category	Legacy PDB format records	Description
_exptl_crystal_grow	REMARK 280	Details about the conditions and methods used to grow the crystal.

Example:

_exptl_crystal_grow.apparatus	?
_exptl_crystal_grow.crystal_id	1
_exptl_crystal_grow.method	'VAPOR DIFFUSION, SITTING DROP'
_exptl_crystal_grow.pH	5.5
_exptl_crystal_grow.pdbx_details	'0.4uL protein, 0.4 uL 100mM Bis-Tri pH 5.5, 25% PEG 3350, 0.2M NaCl equilibrated against a well of 0.5M LiCl'
_exptl_crystal_grow.temp	298

PDBx/mmCIF category	Legacy PDB format records	Description
_exptl_crystal	REMARK 280	Results of experimental measurements on the crystal or crystals used, such as shape, size or density.

Example:

_exptl_crystal.density_Matthews	2.16
_exptl_crystal.density_percent_sol	43.08
_exptl_crystal.id	1

---

Data collection

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn	REMARK 200	Details about the diffraction experiment ambient conditions.

Example:

_diffrn.id	1
_diffrn.ambient_temp	100
_diffrn.crystal_id	1
_diffrn.details	?
_diffrn.pdbx_serial_crystal_experiment	N

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_detector	REMARK 200	Details about the detector used to measure the scattered radiation, including any analyser and post-sample collimation.

Example:

_diffrn_detector.diffrn_id	1
_diffrn_detector.details	mirrors
_diffrn_detector.detector	PIXEL
_diffrn_detector.type	'DECTRIS EIGER X 16M'
_diffrn_detector.pdbx_collection_date	2022-10-07

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_radiation	REMARK 200	Details about the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample.

Example:

_diffrn_radiation.diffrn_id	1
_diffrn_radiation.monochromomator	'Si (111)'
_diffrn_radiation.wavelength_id	1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l	M
_diffrn_radiation.pdbx_diffrn_protocol	'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type	x-ray

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_radiation_wavelength	REMARK 200	Details about the wavelength of the radiation used to measure the diffraction intensities. Several wavelengths can be provided here to describe for example multi-wavelength experiments, such as MAD.

Example:

loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
1	1.0	1.0
2	0.9793	1.0

PDBx/mmCIF category	Legacy PDB format records	Description
_diffrn_source	REMARK 200	Details of the source of radiation used in the diffraction experiment.

Example:

_diffrn_source.current	?
_diffrn_source.details	?
_diffrn_source.diffrn_id	1
_diffrn_source.power	?
_diffrn_source.size	?
_diffrn_source.source	SYNCHROTRON
_diffrn_source.target	?
_diffrn_source.type	'NSLS-II BEAMLINE 17-ID-2'
_diffrn_source.voltage	?
_diffrn_source.pdbx_wavelength_list	0.9793
_diffrn_source.pdbx_synchrotron_beamline	17-ID-2
_diffrn_source.pdbx_synchrotron_site	NSLS-II

PDBx/mmCIF category	Legacy PDB format records	Description
_software	REMARK 3 REMARK 200	Details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation.

Example:

loop_

_software.citation_id

_software.classification

_software.compiler_name

_software.compiler_version

_software.contact_author

_software.contact_author_email

_software.date

_software.description

_software.dependencies

_software.hardware

_software.language

_software.location

_software.mods

_software.name

_software.os

_software.os_version

_software.type

_software.version

_software.pdbx_ordinal

?

refinement

?

?

?

?

?

?

?

?

?

?

?

PHENIX

?

?

?

1.20.1_4487

1

?

'data scaling'

?

?

?

?

?

?

?

?

?

?

?

SCALA

?

?

?

.

2

?

'data reduction'

?

?

?

?

?

?

?

?

?

?

?

XDS

?

?

?

.

3

?

phasing

?

?

?

?

?

?

?

?

?

?

?

PHASER

?

?

?

.

4

---

Data collection and processing statistics

PDBx/mmCIF category	Legacy PDB format records	Description
_reflns	REMARK 200	Overall data collection statistics for the X-ray diffraction experiment.

Example:

_reflns.d_resolution_high	1.660
_reflns.d_resolution_low	62.942
_reflns.pdbx_number_measured_all	560202
_reflns.number_obs	112977
_reflns.pdbx_Rmerge_I_obs	0.040
_reflns.pdbx_netI_over_sigmaI	17.990
_reflns.pdbx_chi_squared	1.115
_reflns.percent_possible_obs	99.400
_reflns.observed_criterion_sigma_I	-3.000
_reflns.pdbx_Rrim_I_all	0.045
_reflns.pdbx_CC_half	0.999
_reflns.B_iso_Wilson_estimate	38.223
_reflns.pdbx_diffrn_id	1
_reflns.pdbx_ordinal	1
_reflns.entry_id	7GT6
_reflns.observed_criterion_sigma_F	?
_reflns.number_all	?
_reflns.pdbx_Rsym_value	?
_reflns.pdbx_redundancy	?

PDBx/mmCIF category	Legacy PDB format records	Description
_reflns_shell	REMARK 200	Data collection statistics for the X-ray diffraction experiment broken into resolution shells.

Example:

loop_
_reflns_shell.pdbx_diffrn_id
_reflns_shell.pdbx_ordinal
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.number_measured_obs
_reflns_shell.number_measured_all
_reflns_shell.number_unique_obs
_reflns_shell.pdbx_rejects
_reflns_shell.Rmerge_I_obs
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.pdbx_Rsym_value
_reflns_shell.pdbx_chi_squared
_reflns_shell.pdbx_redundancy
_reflns_shell.percent_possible_obs
_reflns_shell.pdbx_netI_over_sigmaI_obs
_reflns_shell.number_possible
_reflns_shell.number_unique_all
_reflns_shell.Rmerge_F_all
_reflns_shell.Rmerge_F_obs
_reflns_shell.Rmerge_I_all
_reflns_shell.meanI_over_sigI_all
_reflns_shell.percent_possible_all
_reflns_shell.pdbx_Rrim_I_all
_reflns_shell.pdbx_Rpim_I_all
_reflns_shell.pdbx_CC_half
1	1	1.660	1.760	73562	?	18124	0	0.896	1.320	?	?	?	?	?	18441	?	?	?	?	?	98.300	1.035	?	0.529
1	2	1.760	1.890	73368	?	17113	0	0.473	2.780	?	?	?	?	?	17267	?	?	?	?	?	99.100	0.538	?	0.845
1	3	1.890	2.040	83887	?	15933	0	0.253	5.910	?	?	?	?	?	16040	?	?	?	?	?	99.300	0.282	?	0.968
1	4	2.040	2.230	77815	?	14753	0	0.130	11.180	?	?	?	?	?	14824	?	?	?	?	?	99.500	0.144	?	0.990
1	5	2.230	2.490	69475	?	13360	0	0.079	17.740	?	?	?	?	?	13398	?	?	?	?	?	99.700	0.088	?	0.996
1	6	2.490	2.880	62385	?	11722	0	0.050	27.680	?	?	?	?	?	11738	?	?	?	?	?	99.900	0.056	?	0.998
1	7	2.880	3.520	52823	?	9992	0	0.032	42.650	?	?	?	?	?	9997	?	?	?	?	?	99.900	0.036	?	0.999
1	8	3.520	4.970	40142	?	7731	0	0.024	57.810	?	?	?	?	?	7734	?	?	?	?	?	100.000	0.027	?	0.999
1	9	4.920	62.942	22745	?	4249	0	0.023	62.870	?	?	?	?	?	4252	?	?	?	?	?	99.900	0.025	?	0.999

---

Refinement

PDBx/mmCIF category	Legacy PDB format records	Description
_refine	REMARK 3	Details about the structure-refinement statistics.

Example:

_refine.entry_id	7GT6
_refine.pdbx_refine_id	'X-RAY DIFFRACTION'
_refine.ls_d_res_high	1.6600
_refine.ls_d_res_low	62.9400
_refine.pdbx_ls_sigma_F	0.000
_refine.ls_percent_reflns_obs	99.3700
_refine.ls_number_reflns_obs	56491
_refine.pdbx_ls_cross_valid_method	THROUGHOUT
_refine.pdbx_R_Free_selection_details	RANDOM
_refine.details	'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY'
_refine.ls_R_factor_all	?
_refine.ls_R_factor_obs	0.2007
_refine.ls_R_factor_R_word	0.1996
_refine.ls_R_factor_R_free	0.2276
_refine.ls_percent_reflns_R_free	3.9000
_refine.ls_number_reflns_R_free	2321
_refine.B_iso_mean	37.3880
_refine.aniso_B[1][1]	0.5500
_refine.aniso_B[2][2]	0.5500
_refine.aniso_B[3][3]	-1.7900
_refine.aniso_B[1][2]	0.2800
_refine.aniso_B[1][3]	0.0000
_refine.aniso_B[2][3]	0.0000
_refine.correlation_coeff_Fo_to_Fc	0.9620
_refine.correlation_coeff_Fo_to_Fc_free	0.9530
_refine.pdbx_overall_ESU_R	0.0890
_refine.pdbx_overall_ESU_R_Free	0.0900
_refine.overall_SU_ML	0.0740
_refine.overall_SU_B	2.3210
_refine.solvent_model_details	MASK
_refine.pdbx_solvent_vdw_probe_radii	1.2000
_refine.pdbx_solvent_ion_probe_radii	0.8000
_refine.pdbx_solvent_shrinkage_radii	0.8000
_refine.pdbx_method_to_determine_struct	'MOLECULAR REPLACEMENT'
_refine.pdbx_stereochemistry_target_values	'MAXIMUM LIKELIHOOD'
_refine.B_iso_max	135.070
_refine.B_iso_min	19.500
_refine.pdbx_diffrn_id	1

PDBx/mmCIF category	Legacy PDB format records	Description
_refine_ls_shell	REMARK 3	Details about the results of the least-squares refinement broken down into shells of resolution.

Example:

loop_
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.pdbx_total_number_of_bins_used
_refine_ls_shell.percent_reflns_obs
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_all
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.R_factor_R_free
_refine_ls_shell.percent_reflns_R_free
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.R_factor_R_free_error
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.redundancy_reflns_obs
_refine_ls_shell.pdbx_refine_id
2.500	2.6316	7	97.0	4166	.	0.4102	0.4078	.	135	.	4301	4301	.	'X-RAY DIFFRACTION'
2.6316	2.7964	7	100.0	4242	.	0.3417	0.3548	.	156	.	4398	4398	.	'X-RAY DIFFRACTION'
2.7964	3.0123	7	100.0	4332	.	0.2683	0.3923	.	113	.	4445	4445	.	'X-RAY DIFFRACTION'
3.0123	3.3153	7	100.0	4285	.	0.2135	0.2780	.	158	.	4443	4443	.	'X-RAY DIFFRACTION'
3.3153	3.7947	7	98.0	4266	.	0.2193	0.2524	.	137	.	4403	4403	.	'X-RAY DIFFRACTION'
3.7947	4.7796	7	99.0	4312	.	0.1696	0.2265	.	156	.	4468	4468	.	'X-RAY DIFFRACTION'
4.7796	39.7236	7	100.0	4512	.	0.1794	0.1675	.	160	.	4672	4672	.	'X-RAY DIFFRACTION'

PDBx/mmCIF category	Legacy PDB format records	Description
_refine_ls_restr	REMARK 3	Details about the restraints applied to various classes of parameters during the least-squares refinement.

Notes:

• The following PDB to PDB/mmCIF Data Item Correspondences provide description of the restraint types: http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html

Example:

loop_
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.pdbx_restraint_function
'X-RAY DIFFRACTION'	r_bond_refined_d	3714	0.048	0.025	?	?
'X-RAY DIFFRACTION'	r_bond_other_d	2730	0.001	0.015	?	?
'X-RAY DIFFRACTION'	r_angle_refined_deg	3919	1.717	1.662	?	?
'X-RAY DIFFRACTION'	r_angle_other_deg	6334	1.410	1.601	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_1_deg	355	6.689	5.000	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_2_deg	169	29.721	21.361	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_3_deg	545	14.366	15.000	?	?
'X-RAY DIFFRACTION'	r_dihedral_angle_4_deg	26	24.117	15.000	?	?
'X-RAY DIFFRACTION'	r_chiral_restr	357	0.088	0.200	?	?
'X-RAY DIFFRACTION'	r_gen_planes_refined	3323	0.009	0.020	?	?
'X-RAY DIFFRACTION'	r_gen_planes_other	705	0.001	0.020	?	?
'X-RAY DIFFRACTION'	r_mcbond_it	1792	3.161	3.442	?	?
'X-RAY DIFFRACTION'	r_mcbond_other	1753	3.149	3.416	?	?
'X-RAY DIFFRACTION'	r_mcangle_it	1735	4.416	5.214	?	?

PDBx/mmCIF category	Legacy PDB format records	Description
_pdbx_initial_refinement_model	N/A	The starting model(s) used in structure determination.

Example:

_pdbx_initial_refinement_model.id	1
_pdbx_initial_refinement_model.entity_id_list	1
_pdbx_initial_refinement_model.type	'experimental model'
_pdbx_initial_refinement_model.source_name	PDB
_pdbx_initial_refinement_model.accession_code	6HA3
_pdbx_initial_refinement_model.details	?

---

Crystallographic and Coordinate Transformation Section

PDBx/mmCIF category	Legacy PDB format records	Description
_symmetry	CRYST1	Details about the space group symmetry.

Example:

_symmetry.entry_id	8VCW
_symmeetry.cell_setting	?
_symmetry.Int_Tables_number	19
_symmetry.space_group_name_Hall	?
_symmetry.space_group_name_H-M	'P 21 21 21'
_symmeetry.pdbx_full_space_group_name_H-M	?

PDBx/mmCIF category	Legacy PDB format records	Description
_cell	CRYST1	Details about the crystallographic cell parameters.

Example:

_cell.angle_alpha	90.00
_cell.angle_beta	90.00
_cell.angle_gamma	90.00
_cell.entry_id	8VCW
_cell.length_a	38.209
_cell.length_b	50.7776
_cell.length_c	161.878
_cell.Z_PDB	4

PDBx/mmCIF category	Legacy PDB format records	Description
_atom_sites	SCALE	Details about the matrix used to transform fractional coordinates to Cartesian coordinates.

Example:

_atom_sites.entry_id	8VCW
_atom_sites.Cartn_transf_matrix[1][1]	?
_atom_sites.Cartn_transf_matrix[1][2]	?
_atom_sites.Cartn_transf_matrix[1][3]	?
_atom_sites.Cartn_transf_matrix[2][1]	?
_atom_sites.Cartn_transf_matrix[2][2]	?
_atom_sites.Cartn_transf_matrix[2][3]	?
_atom_sites.Cartn_transf_matrix[3][1]	?
_atom_sites.Cartn_transf_matrix[3][2]	?
_atom_sites.Cartn_transf_matrix[3][3]	?
_atom_sites.Cartn_transf_vector[1]	?
_atom_sites.Cartn_transf_vector[2]	?
_atom_sites.Cartn_transf_vector[3]	?
_atom_sites.Cart_transform_axes	?
_atom_sites.fract_transf_matrix[1][1]	0.026172
_atom_sites.fract_transf_matrix[1][2]	0.000000
_atom_sites.fract_transf_matrix[1][3]	0.000000
_atom_sites.fract_transf_matrix[2][1]	0.000000
_atom_sites.fract_transf_matrix[2][2]	0.019694
_atom_sites.fract_transf_matrix[2][3]	0.000000
_atom_sites.fract_transf_matrix[3][1]	0.000000
_atom_sites.fract_transf_matrix[3][2]	0.000000
_atom_sites.fract_transf_matrix[3][3]	0.006177
_atom_sites.fract_transf_vector[1]	0.00000
_atom_sites.fract_transf_vector[2]	0.00000
_atom_sites.fract_transf_vector[3]	0.00000