9S57 | pdb_00009s57

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QQI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	200 mM magnesium formate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.32

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 EIGER2 XE 16M		2024-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.568	58.278	66.7	0.265	0.272	0.061	0.998	7.5	19.6		26510

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.568	1.796	10		2.028	2.086	0.485	0.592	1.6	18.4

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	1.569	58.278	26509	1509	66.807	0.175	0.1708	0.1806	0.2388	0.2463	20.333

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]
0.005		-0.013	-0.123		0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.65
r_dihedral_angle_3_deg	13.11
r_dihedral_angle_2_deg	8.582
r_dihedral_angle_1_deg	7.956
r_lrange_it	6.81
r_lrange_other	6.724
r_scangle_it	4.784
r_scangle_other	4.782
r_scbond_it	3.088
r_scbond_other	3.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.65
r_dihedral_angle_3_deg	13.11
r_dihedral_angle_2_deg	8.582
r_dihedral_angle_1_deg	7.956
r_lrange_it	6.81
r_lrange_other	6.724
r_scangle_it	4.784
r_scangle_other	4.782
r_scbond_it	3.088
r_scbond_other	3.086
r_mcangle_it	3.049
r_mcangle_other	3.048
r_mcbond_it	1.946
r_mcbond_other	1.946
r_angle_refined_deg	1.526
r_angle_other_deg	0.53
r_symmetry_xyhbond_nbd_refined	0.241
r_nbd_other	0.225
r_xyhbond_nbd_refined	0.223
r_symmetry_nbd_refined	0.215
r_nbd_refined	0.199
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.18
r_xyhbond_nbd_other	0.132
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.039
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2528
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms

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.