9Q5R | pdb_00009q5r

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
2.49	50.5

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	2025-02-12	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	2.3	50.4	98.5	0.098	0.995	5.2	4		195162			58.9

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	2.3	2.38	99.3		1.93	0.18	0.6

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	2.3	30.471	48185	2419	98.166	0.217	0.214	0.2143	0.2725	0.2722	Random Selection	70.179

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]
1.241	0.621		1.241		-4.026

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.082
r_dihedral_angle_3_deg	16.931
r_dihedral_angle_6_deg	13.602
r_lrange_it	12.806
r_scangle_it	9.964
r_mcangle_it	8.147
r_dihedral_angle_1_deg	7.662
r_scbond_it	6.831
r_mcbond_it	5.607
r_angle_refined_deg	1.635

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.082
r_dihedral_angle_3_deg	16.931
r_dihedral_angle_6_deg	13.602
r_lrange_it	12.806
r_scangle_it	9.964
r_mcangle_it	8.147
r_dihedral_angle_1_deg	7.662
r_scbond_it	6.831
r_mcbond_it	5.607
r_angle_refined_deg	1.635
r_nbtor_refined	0.313
r_nbd_refined	0.24
r_symmetry_nbd_refined	0.201
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.123
r_symmetry_xyhbond_nbd_refined	0.105
r_metal_ion_refined	0.076
r_gen_planes_refined	0.006
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7664
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	151

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.