9VF3 | pdb_00009vf3

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5R7Y

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.2 M LiCl, 0.1 M Bis-Tris pH 6.5, 13%(w/v) polyethylene glycol 8000

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.53

Symmetry
Space Group	I 1 2 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU		2022-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54187

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.964	28.134	91.99	0.996	11.91	2.9		17882

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.964	2.034			0.897

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.964	28.134	17869	899	91.966	0.221	0.2186	0.2244	0.2597	0.2683	23.435

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]
-0.141		0.225	0.872		-0.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.308
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	14.698
r_dihedral_angle_1_deg	8.086
r_lrange_it	4.733
r_lrange_other	4.719
r_scangle_it	3.132
r_scangle_other	3.132
r_mcangle_it	2.936
r_mcangle_other	2.936

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.308
r_dihedral_angle_4_deg	18.495
r_dihedral_angle_3_deg	14.698
r_dihedral_angle_1_deg	8.086
r_lrange_it	4.733
r_lrange_other	4.719
r_scangle_it	3.132
r_scangle_other	3.132
r_mcangle_it	2.936
r_mcangle_other	2.936
r_scbond_it	1.964
r_scbond_other	1.963
r_mcbond_it	1.839
r_mcbond_other	1.834
r_angle_refined_deg	1.523
r_angle_other_deg	1.305
r_nbd_refined	0.21
r_nbd_other	0.195
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2323
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	36

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.