9Q4E | pdb_00009q4e

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
2.64	53.4

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	2.1	36.34	99.7	0.08	0.999	8.5	5.7		67938			57.8

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	2.1	2.21	99.9		4.11	0.16	0.5

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	2.1	30.723	67848	3580	99.573	0.251	0.2484	0.2482	0.3009	0.3013	Random Selection	74.321

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]
1.307	0.654		1.307		-4.241

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.644
r_dihedral_angle_3_deg	14.677
r_dihedral_angle_6_deg	11.058
r_dihedral_angle_1_deg	6.798
r_lrange_it	5.592
r_scangle_it	2.81
r_mcangle_it	2.515
r_scbond_it	1.617
r_mcbond_it	1.48
r_angle_refined_deg	1.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.644
r_dihedral_angle_3_deg	14.677
r_dihedral_angle_6_deg	11.058
r_dihedral_angle_1_deg	6.798
r_lrange_it	5.592
r_scangle_it	2.81
r_mcangle_it	2.515
r_scbond_it	1.617
r_mcbond_it	1.48
r_angle_refined_deg	1.022
r_nbtor_refined	0.302
r_nbd_refined	0.206
r_symmetry_nbd_refined	0.155
r_xyhbond_nbd_refined	0.131
r_metal_ion_refined	0.121
r_symmetry_xyhbond_nbd_refined	0.115
r_chiral_restr	0.088
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7650
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	160

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.