9Y57 | pdb_00009y57

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6X3N

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10% PEG 20000, 20% PEG MME 550, 0.03 M Sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, and 0.1 M MES/Imidazole pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.34

Symmetry
Space Group	P 21 21 2

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		2022-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9794	APS	21-ID-D

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	50	97.7	0.042	0.994	53.2	9.9		55896

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.42			0.133	0.987

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	1.4	42.309	55890	2734	97.628	0.157	0.1559	0.1558	0.1724	0.1722	15.6

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]
-0.002			0.108		-0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.666
r_dihedral_angle_6_deg	15.838
r_dihedral_angle_3_deg	12.101
r_lrange_it	8.197
r_lrange_other	7.814
r_dihedral_angle_1_deg	7.377
r_scangle_it	4.821
r_scangle_other	4.819
r_mcangle_other	3.43
r_mcangle_it	3.427

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.666
r_dihedral_angle_6_deg	15.838
r_dihedral_angle_3_deg	12.101
r_lrange_it	8.197
r_lrange_other	7.814
r_dihedral_angle_1_deg	7.377
r_scangle_it	4.821
r_scangle_other	4.819
r_mcangle_other	3.43
r_mcangle_it	3.427
r_scbond_it	3.197
r_scbond_other	3.196
r_mcbond_it	2.135
r_mcbond_other	2.133
r_angle_refined_deg	2.082
r_angle_other_deg	0.661
r_nbd_refined	0.234
r_xyhbond_nbd_refined	0.223
r_nbd_other	0.209
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.169
r_symmetry_nbd_refined	0.134
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2227
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	53

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.