9T72 | pdb_00009t72

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M SPG pH 6.0, 25% w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.3

Symmetry
Space Group	C 1 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 EIGER X 16M		2023-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.7	48.58	98.88	0.999	15.95	6.9		29117

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	1.7	1.761			0.704

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	48.58	29117	1419	98.882	0.196	0.1938	0.2006	0.2431	0.2441	39.106

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]
0.465		1.466	-1.745		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.354
r_dihedral_angle_3_deg	16.072
r_dihedral_angle_2_deg	11.001
r_lrange_other	8.102
r_lrange_it	8.093
r_dihedral_angle_1_deg	7.261
r_scangle_it	6.537
r_scangle_other	6.535
r_scbond_it	4.478
r_scbond_other	4.477

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.354
r_dihedral_angle_3_deg	16.072
r_dihedral_angle_2_deg	11.001
r_lrange_other	8.102
r_lrange_it	8.093
r_dihedral_angle_1_deg	7.261
r_scangle_it	6.537
r_scangle_other	6.535
r_scbond_it	4.478
r_scbond_other	4.477
r_mcangle_it	4.287
r_mcangle_other	4.286
r_dihedral_angle_other_3_deg	3.251
r_mcbond_it	3.19
r_mcbond_other	3.187
r_angle_refined_deg	1.534
r_angle_other_deg	0.533
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.22
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.188
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.086
r_symmetry_xyhbond_nbd_refined	0.085
r_chiral_restr	0.073
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	41

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.