9OT5 | pdb_00009ot5

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% PEG4000, 0.1 M MES, 5% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.57

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		2023-11-29	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)	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	2.29	39.75	100	0.989	4.89	13.5		31517

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	2.29	2.33	100		0.0332	0.03457	0.96	0.356		12.9

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	2.5	39.743	24278	1286	99.951	0.198	0.1947	0.1967	0.2455	0.2471	46.474

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]
-3.466			4.175		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.571
r_dihedral_angle_3_deg	15.744
r_dihedral_angle_6_deg	14.446
r_lrange_it	8.537
r_dihedral_angle_1_deg	7.571
r_scangle_it	6.499
r_scbond_it	4.574
r_mcangle_it	4.449
r_mcbond_it	2.989
r_angle_refined_deg	2.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.571
r_dihedral_angle_3_deg	15.744
r_dihedral_angle_6_deg	14.446
r_lrange_it	8.537
r_dihedral_angle_1_deg	7.571
r_scangle_it	6.499
r_scbond_it	4.574
r_mcangle_it	4.449
r_mcbond_it	2.989
r_angle_refined_deg	2.049
r_nbtor_refined	0.318
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.213
r_xyhbond_nbd_refined	0.154
r_ncsr_local_group_1	0.13
r_symmetry_xyhbond_nbd_refined	0.121
r_chiral_restr	0.118
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4622
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	61

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.