9OT4 | pdb_00009ot4

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YB7

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	11% PEG 4000, 0.1 M MES, 5% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.14

Symmetry
Space Group	P 21 21 21

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 X 16M		2023-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.65	56.75	99.98	0.177	0.184	0.05	0.997	8.4	13.5		84761

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	1.65	1.68			0.34

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	2.1	56.749	41418	968	99.947	0.192	0.1909	0.1921	0.2264	0.2277	36.606

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]
-2.759			3.602		-0.843

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.58
r_dihedral_angle_3_deg	12.683
r_dihedral_angle_1_deg	6.916
r_lrange_it	6.261
r_dihedral_angle_2_deg	6.009
r_scangle_it	4.55
r_scbond_it	3.114
r_mcangle_it	2.839
r_angle_refined_deg	1.897
r_mcbond_it	1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.58
r_dihedral_angle_3_deg	12.683
r_dihedral_angle_1_deg	6.916
r_lrange_it	6.261
r_dihedral_angle_2_deg	6.009
r_scangle_it	4.55
r_scbond_it	3.114
r_mcangle_it	2.839
r_angle_refined_deg	1.897
r_mcbond_it	1.88
r_nbtor_refined	0.318
r_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_refined	0.184
r_xyhbond_nbd_refined	0.131
r_ncsr_local_group_1	0.117
r_chiral_restr	0.108
r_ext_dist_refined_b	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4581
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms	34

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.