9V9F | pdb_00009v9f

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		290	0.05 M Lithium acetate, 0.1 M HEPES 7.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.44

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 EIGER X 16M		2024-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97923	SSRF	BL19U1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	46.964	100	0.088	22.4	12.4		37385

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.256	9.9

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	THROUGHOUT	2	46.964	37318	1844	99.946	0.197	0.1961	0.2017	0.2185	0.2238	17.93

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]
-0.288			0.488		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.176
r_dihedral_angle_4_deg	13.899
r_dihedral_angle_3_deg	11.578
r_dihedral_angle_1_deg	6.013
r_lrange_it	2.84
r_lrange_other	2.557
r_angle_other_deg	2.306
r_angle_refined_deg	1.136
r_mcangle_it	0.698
r_mcangle_other	0.698

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.176
r_dihedral_angle_4_deg	13.899
r_dihedral_angle_3_deg	11.578
r_dihedral_angle_1_deg	6.013
r_lrange_it	2.84
r_lrange_other	2.557
r_angle_other_deg	2.306
r_angle_refined_deg	1.136
r_mcangle_it	0.698
r_mcangle_other	0.698
r_scangle_it	0.412
r_scangle_other	0.412
r_mcbond_it	0.368
r_mcbond_other	0.368
r_symmetry_nbd_other	0.202
r_scbond_it	0.196
r_scbond_other	0.196
r_nbd_refined	0.17
r_nbtor_refined	0.162
r_symmetry_nbd_refined	0.147
r_nbd_other	0.133
r_xyhbond_nbd_refined	0.085
r_symmetry_xyhbond_nbd_refined	0.062
r_symmetry_nbtor_other	0.06
r_chiral_restr	0.048
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.013
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4021
Nucleic Acid Atoms
Solvent Atoms	531
Heterogen Atoms	51

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.