9T52 | pdb_00009t52

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	6.5	293	0.1 M Bis-Tris, pH 6.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.43

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		2023-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03272	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	1.76	46.05	99.05	0.999	16.32	14		110393

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	1.76	1.823			0.75

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	1.76	46.05	110393	5651	99.011	0.176	0.1741	0.1881	0.2126	0.223	29.7

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]
-0.532		-1.693	-1.318		2.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.324
r_dihedral_angle_3_deg	15.884
r_dihedral_angle_2_deg	7.952
r_dihedral_angle_1_deg	6.982
r_lrange_it	6.441
r_lrange_other	6.414
r_scangle_it	5.068
r_scangle_other	5.068
r_scbond_it	3.35
r_scbond_other	3.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.324
r_dihedral_angle_3_deg	15.884
r_dihedral_angle_2_deg	7.952
r_dihedral_angle_1_deg	6.982
r_lrange_it	6.441
r_lrange_other	6.414
r_scangle_it	5.068
r_scangle_other	5.068
r_scbond_it	3.35
r_scbond_other	3.35
r_dihedral_angle_other_2_deg	3.323
r_mcangle_it	3.26
r_mcangle_other	3.259
r_mcbond_it	2.34
r_mcbond_other	2.34
r_dihedral_angle_other_3_deg	2.244
r_angle_refined_deg	1.404
r_angle_other_deg	0.486
r_nbd_refined	0.208
r_symmetry_nbd_other	0.195
r_nbd_other	0.19
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.162
r_xyhbond_nbd_refined	0.142
r_symmetry_nbd_refined	0.139
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.07
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9400
Nucleic Acid Atoms
Solvent Atoms	633
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.