9WIV | pdb_00009wiv

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VB8

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.04 M Citric Acid/0.06 M Bis-Tris Propane pH 6.4; 20% PEG 3350; 5% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.18

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 EIGER2 S 9M		2025-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979	SSRF	BL02U1

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	2.9	94.38	97.7	0.996	9.7	6.9		15690

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	2.9	3.08			0.656

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.9	59.577	15668	778	97.723	0.218	0.2165	0.2508	87.535

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]
1.192		0.469	-4.399		2.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.942
r_dihedral_angle_6_deg	11.458
r_lrange_it	7.643
r_lrange_other	7.643
r_dihedral_angle_1_deg	5.294
r_dihedral_angle_2_deg	3.754
r_scangle_it	3.71
r_scangle_other	3.709
r_mcangle_it	3.43
r_mcangle_other	3.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.942
r_dihedral_angle_6_deg	11.458
r_lrange_it	7.643
r_lrange_other	7.643
r_dihedral_angle_1_deg	5.294
r_dihedral_angle_2_deg	3.754
r_scangle_it	3.71
r_scangle_other	3.709
r_mcangle_it	3.43
r_mcangle_other	3.43
r_scbond_it	2.135
r_scbond_other	2.134
r_mcbond_it	2.007
r_mcbond_other	2.007
r_angle_refined_deg	0.849
r_angle_other_deg	0.322
r_nbd_refined	0.199
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.174
r_nbd_other	0.156
r_ncsr_local_group_1	0.128
r_xyhbond_nbd_refined	0.123
r_symmetry_nbd_refined	0.123
r_symmetry_xyhbond_nbd_refined	0.082
r_symmetry_nbtor_other	0.074
r_dihedral_angle_other_2_deg	0.051
r_chiral_restr	0.043
r_ext_dist_refined_b	0.042
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5550
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	52

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.