9Q4A | pdb_00009q4a

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 BL12-1	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	2.5	37.84	99.7	0.26	0.987	6.3	5.7		40465			56.1

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	2.5	2.63	99.3		3.66	0.12	0.4	5.6

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	2.5	30.641	40406	1925	99.601	0.234	0.2317	0.2319	0.2725	0.2734	Random Selection	62.896

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]
1.16	0.58		1.16		-3.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.441
r_dihedral_angle_2_deg	13.868
r_dihedral_angle_6_deg	10.627
r_dihedral_angle_1_deg	6.529
r_lrange_it	4.607
r_scangle_it	2.268
r_mcangle_it	1.971
r_scbond_it	1.273
r_mcbond_it	1.128
r_angle_refined_deg	0.988

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.441
r_dihedral_angle_2_deg	13.868
r_dihedral_angle_6_deg	10.627
r_dihedral_angle_1_deg	6.529
r_lrange_it	4.607
r_scangle_it	2.268
r_mcangle_it	1.971
r_scbond_it	1.273
r_mcbond_it	1.128
r_angle_refined_deg	0.988
r_nbtor_refined	0.301
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.138
r_symmetry_xyhbond_nbd_refined	0.122
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.082
r_metal_ion_refined	0.035
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7660
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms	156

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.