9Q4C | pdb_00009q4c

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	PEG 4000, Glycerol, ethyleneglycol, bicine/tris

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.1

Symmetry
Space Group	P 32 2 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 XE 16M	Kirkpatrick-Baez (KB) optical mirrors	2024-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	37.81	99	0.103	0.998	6.7	5.7		58396			62.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	100		3.38	0.17	0.5	5.8

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	2.2	30.668	58288	2921	98.854	0.224	0.222	0.2223	0.2715	0.2716	Random Selection	75.672

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]
1.123	0.562		1.123		-3.643

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.869
r_dihedral_angle_3_deg	14.762
r_dihedral_angle_6_deg	11.442
r_lrange_it	7.588
r_dihedral_angle_1_deg	6.878
r_scangle_it	4.75
r_mcangle_it	3.985
r_scbond_it	2.838
r_mcbond_it	2.456
r_angle_refined_deg	1.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.869
r_dihedral_angle_3_deg	14.762
r_dihedral_angle_6_deg	11.442
r_lrange_it	7.588
r_dihedral_angle_1_deg	6.878
r_scangle_it	4.75
r_mcangle_it	3.985
r_scbond_it	2.838
r_mcbond_it	2.456
r_angle_refined_deg	1.105
r_nbtor_refined	0.304
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.141
r_xyhbond_nbd_refined	0.124
r_metal_ion_refined	0.118
r_chiral_restr	0.094
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7647
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	158

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.