9VOX | pdb_00009vox

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Implemented by subcontractors

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	8.0% v/v ethylene glycol; 0.1M HEPES pH 7.25; 10% w/v PEG 10K

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.5

Symmetry
Space Group	I 2 3

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 EIGER2 X CdTe 16M		2024-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.686	102.314	97.1	0.207	0.207	17	41.6		13818

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.686	2.732	100		4.748	4.748	1.3	43

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 (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	2.69	102.31	13095	714	97.04	0.214	0.21155	0.2132	0.25779	0.2559	RANDOM	71.536

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.771
r_dihedral_angle_3_deg	12.552
r_dihedral_angle_4_deg	10.399
r_long_range_B_refined	8.009
r_long_range_B_other	8.007
r_mcangle_it	6.361
r_mcangle_other	6.359
r_dihedral_angle_1_deg	6.243
r_scangle_other	4.983
r_mcbond_it	3.768

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.771
r_dihedral_angle_3_deg	12.552
r_dihedral_angle_4_deg	10.399
r_long_range_B_refined	8.009
r_long_range_B_other	8.007
r_mcangle_it	6.361
r_mcangle_other	6.359
r_dihedral_angle_1_deg	6.243
r_scangle_other	4.983
r_mcbond_it	3.768
r_mcbond_other	3.757
r_scbond_it	2.949
r_scbond_other	2.949
r_angle_refined_deg	1.328
r_angle_other_deg	1.095
r_chiral_restr	0.053
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2408
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	30

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.