9V5K | pdb_00009v5k

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V3E

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PEG4000, Sodium citrate, Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.45

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2023-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9792	SSRF	BL18U1

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	2.37	50	96.1	0.972	6.4	7.2		29431

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	2.37	2.49			0.455

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	2.37	50	29238	1463	94.993	0.229	0.227	0.2314	0.2618	0.2595	48.023

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]
-0.32			0.993		-0.672

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.055
r_dihedral_angle_4_deg	20.164
r_dihedral_angle_3_deg	19.503
r_lrange_other	11.974
r_lrange_it	11.972
r_scangle_it	6.774
r_scangle_other	6.773
r_mcangle_it	5.924
r_mcangle_other	5.923
r_dihedral_angle_1_deg	5.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.055
r_dihedral_angle_4_deg	20.164
r_dihedral_angle_3_deg	19.503
r_lrange_other	11.974
r_lrange_it	11.972
r_scangle_it	6.774
r_scangle_other	6.773
r_mcangle_it	5.924
r_mcangle_other	5.923
r_dihedral_angle_1_deg	5.818
r_scbond_it	4.35
r_scbond_other	4.349
r_mcbond_it	3.987
r_mcbond_other	3.987
r_angle_refined_deg	1.519
r_angle_other_deg	1.207
r_symmetry_xyhbond_nbd_refined	0.382
r_symmetry_nbd_refined	0.221
r_nbd_other	0.214
r_nbd_refined	0.208
r_xyhbond_nbd_other	0.195
r_symmetry_nbd_other	0.181
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.158
r_ncsr_local_group_1	0.156
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3569
Nucleic Acid Atoms
Solvent Atoms	92
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.