9V9M | pdb_00009v9m

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	0.1M Sodium cacodylate pH 6.5; 22% w/v PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.46

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	RIGAKU HyPix-6000HE		2023-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.5	23.631	99.7	0.063	24.32	4.3		19687

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	2.5	2.59			0.218	4.66

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	2.501	23.631	19627	1010	99.715	0.225	0.2231	0.2264	0.256	0.2626	17.295

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]
-0.155			-0.008		0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.596
r_dihedral_angle_3_deg	13.507
r_dihedral_angle_4_deg	11.928
r_dihedral_angle_1_deg	5.05
r_lrange_it	1.463
r_lrange_other	1.368
r_angle_refined_deg	1.132
r_angle_other_deg	1.097
r_mcangle_it	0.468
r_mcangle_other	0.468

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.596
r_dihedral_angle_3_deg	13.507
r_dihedral_angle_4_deg	11.928
r_dihedral_angle_1_deg	5.05
r_lrange_it	1.463
r_lrange_other	1.368
r_angle_refined_deg	1.132
r_angle_other_deg	1.097
r_mcangle_it	0.468
r_mcangle_other	0.468
r_scangle_it	0.273
r_scangle_other	0.273
r_mcbond_it	0.248
r_mcbond_other	0.248
r_symmetry_xyhbond_nbd_refined	0.222
r_symmetry_nbd_other	0.162
r_nbtor_refined	0.157
r_nbd_refined	0.15
r_scbond_it	0.136
r_scbond_other	0.136
r_nbd_other	0.124
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.083
r_symmetry_nbd_refined	0.071
r_chiral_restr	0.035
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4023
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	65

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.