9V5Y | pdb_00009v5y

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
2	38.55

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 R 4M		2024-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.01200	Photon Factory	BL-1A

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	1.57	63.64	99.9	0.997	7.8	3.5		122920			16.52

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	1.57	1.6			0.544	1

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	1.57	63.64	116554	6216	99.77	0.16867	0.16726	0.1813	0.19499	0.208	RANDOM	23.671

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]
-0.42		-0.79	0.26		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.295
r_long_range_B_refined	7.41
r_long_range_B_other	7.321
r_dihedral_angle_1_deg	6.069
r_scangle_other	5.715
r_scbond_it	3.717
r_scbond_other	3.716
r_dihedral_angle_2_deg	3.517
r_mcangle_other	3.141
r_mcangle_it	3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.295
r_long_range_B_refined	7.41
r_long_range_B_other	7.321
r_dihedral_angle_1_deg	6.069
r_scangle_other	5.715
r_scbond_it	3.717
r_scbond_other	3.716
r_dihedral_angle_2_deg	3.517
r_mcangle_other	3.141
r_mcangle_it	3.14
r_mcbond_it	2.073
r_mcbond_other	2.069
r_angle_refined_deg	1.938
r_angle_other_deg	0.643
r_chiral_restr	0.098
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	561
Heterogen Atoms	81

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.