9WOM | pdb_00009wom

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6WRH

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.05 M Ammonium sulfate, 0.1 M Sodium citrate (No pH), and 15% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.56	56.7

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2023-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97857	SSRF	BL10U2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.56	73.02	99.1	0.176	0.213	0.086	0.973	7.2	6.2		25404

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.67	98.2		0.727	0.932	0.571	0.612	2	4.8

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.56	73.02	25367	1271	98.939	0.22	0.22039	0.2173	0.2223	0.278	0.2743	RANDOM	24.887

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.178		0.87	1.513		-2.824

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.511
r_dihedral_angle_2_deg	11.831
r_dihedral_angle_3_deg	11.399
r_dihedral_angle_1_deg	5.652
r_lrange_it	2.928
r_lrange_other	2.915
r_mcangle_it	1.445
r_mcangle_other	1.445
r_scangle_it	0.987
r_scangle_other	0.987

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.511
r_dihedral_angle_2_deg	11.831
r_dihedral_angle_3_deg	11.399
r_dihedral_angle_1_deg	5.652
r_lrange_it	2.928
r_lrange_other	2.915
r_mcangle_it	1.445
r_mcangle_other	1.445
r_scangle_it	0.987
r_scangle_other	0.987
r_angle_refined_deg	0.802
r_mcbond_it	0.78
r_mcbond_other	0.779
r_angle_other_deg	0.625
r_scbond_it	0.513
r_scbond_other	0.513
r_symmetry_nbd_other	0.2
r_nbd_other	0.191
r_nbd_refined	0.181
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.17
r_metal_ion_refined	0.164
r_xyhbond_nbd_refined	0.117
r_symmetry_nbd_refined	0.086
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.034
r_gen_planes_other	0.004
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5014
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	85

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.