9VF2 | pdb_00009vf2

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, HANGING DROP		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
1.96	37.32

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		2022-08-18	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	1.97	27.516	91.66	0.996	12.68	3.2		17881

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	1.97	2.04			0.942

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	1.97	27.516	17587	908	91.661	0.231	0.2285	0.2338	0.2743	0.276	26.974

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]
-0.546		0.604	0.971		-0.611

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.98
r_dihedral_angle_4_deg	16.278
r_dihedral_angle_3_deg	14.95
r_dihedral_angle_1_deg	7.886
r_lrange_it	5.306
r_lrange_other	5.27
r_scangle_it	3.546
r_scangle_other	3.545
r_mcangle_it	3.383
r_mcangle_other	3.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.98
r_dihedral_angle_4_deg	16.278
r_dihedral_angle_3_deg	14.95
r_dihedral_angle_1_deg	7.886
r_lrange_it	5.306
r_lrange_other	5.27
r_scangle_it	3.546
r_scangle_other	3.545
r_mcangle_it	3.383
r_mcangle_other	3.382
r_scbond_it	2.232
r_scbond_other	2.232
r_mcbond_other	2.129
r_mcbond_it	2.128
r_angle_refined_deg	1.523
r_angle_other_deg	1.302
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.186
r_symmetry_nbd_other	0.183
r_nbd_other	0.171
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.134
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.067
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	2347
Nucleic Acid Atoms
Solvent Atoms	87
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.