9P5C | pdb_00009p5c

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9P4B

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	25% PEG 8K, 200 mM sodium acetate, 85 mM sodium cacodylate pH 6.5 and 12% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.98

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		2022-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.03322	APS	23-ID-D

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.93	34	99	0.082	0.044	0.997	9.6	4.2		43910

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.98	99.7		1.181	0.169	0.39	1.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.93	33.792	43849	2148	98.766	0.174	0.1723	0.1841	0.2151	0.2258	Random selection	37.567

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]
0.234			0.62		-0.854

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.26
r_dihedral_angle_3_deg	14.927
r_lrange_it	7.523
r_lrange_other	7.464
r_dihedral_angle_2_deg	7.222
r_dihedral_angle_1_deg	6.512
r_scangle_it	5.697
r_scangle_other	5.696
r_mcangle_it	4.106
r_mcangle_other	4.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.26
r_dihedral_angle_3_deg	14.927
r_lrange_it	7.523
r_lrange_other	7.464
r_dihedral_angle_2_deg	7.222
r_dihedral_angle_1_deg	6.512
r_scangle_it	5.697
r_scangle_other	5.696
r_mcangle_it	4.106
r_mcangle_other	4.106
r_scbond_it	3.572
r_scbond_other	3.572
r_mcbond_it	2.749
r_mcbond_other	2.741
r_angle_refined_deg	1.311
r_angle_other_deg	0.446
r_symmetry_xyhbond_nbd_refined	0.232
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.194
r_xyhbond_nbd_refined	0.184
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.176
r_nbd_other	0.164
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.065
r_bond_refined_d	0.006
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	4200
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms

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.