9Q4B | pdb_00009q4b

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
2.6	52.8

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 BL12-1	0.97946	SSRL	BL12-1

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	2.19	37.75	99.7	0.069	0.999	10.4	5.7		58865			65.8

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	2.19	2.31	98.9		2.92	0.16	0.5	5.7

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	2.194	30.414	58756	2849	99.554	0.24	0.2371	0.2373	0.2926	0.2927	Random Selection	79.673

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]
1.511	0.755		1.511		-4.901

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.553
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_6_deg	10.264
r_dihedral_angle_1_deg	6.52
r_lrange_it	5.574
r_scangle_it	2.97
r_mcangle_it	2.622
r_scbond_it	1.712
r_mcbond_it	1.544
r_angle_refined_deg	0.988

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.553
r_dihedral_angle_3_deg	14.095
r_dihedral_angle_6_deg	10.264
r_dihedral_angle_1_deg	6.52
r_lrange_it	5.574
r_scangle_it	2.97
r_mcangle_it	2.622
r_scbond_it	1.712
r_mcbond_it	1.544
r_angle_refined_deg	0.988
r_nbtor_refined	0.3
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.126
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.083
r_metal_ion_refined	0.019
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7638
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	154

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.