9V5Z | pdb_00009v5z

X-RAY DIFFRACTION

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris-HCl pH 8.0, 20%(w/v) PEG6000, and 0.2 M CaCl2

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.61

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2024-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90000	SPring-8	BL44XU

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.58	45.01	96	0.991	6.2	3.1		114534			16.32

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.6			0.505	1.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1.58	45.01	108547	5807	95.88	0.16416	0.163	0.1774	0.18567	0.1983	RANDOM	24.954

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]
-0.05		-0.94	0.64		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.692
r_dihedral_angle_2_deg	8.693
r_long_range_B_refined	7.417
r_long_range_B_other	7.369
r_dihedral_angle_1_deg	6.077
r_scangle_other	5.645
r_scbond_it	3.592
r_scbond_other	3.592
r_mcangle_other	3.147
r_mcangle_it	3.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.692
r_dihedral_angle_2_deg	8.693
r_long_range_B_refined	7.417
r_long_range_B_other	7.369
r_dihedral_angle_1_deg	6.077
r_scangle_other	5.645
r_scbond_it	3.592
r_scbond_other	3.592
r_mcangle_other	3.147
r_mcangle_it	3.146
r_mcbond_it	2.069
r_mcbond_other	2.069
r_angle_refined_deg	1.873
r_angle_other_deg	0.616
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6570
Nucleic Acid Atoms
Solvent Atoms	475
Heterogen Atoms	165

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.