9T0R | pdb_00009t0r

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	7.5	293	0.2 M lithium chloride, 0.1 M Tris, 20% PEG 6000, 10% Ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.67

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		2025-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	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	1.55	46.04	98.79	0.999	10.84	7		201147

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	1.55	1.605			0.582

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	1.55	46.04	201144	10007	98.83	0.218	0.2163	0.2335	0.245	0.2628	26.718

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]
-2.223		0.62	-1.373		3.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.471
r_dihedral_angle_3_deg	15.461
r_dihedral_angle_2_deg	8.476
r_dihedral_angle_1_deg	7.172
r_lrange_it	6.732
r_lrange_other	6.719
r_scangle_it	5.418
r_scangle_other	5.418
r_scbond_it	3.534
r_scbond_other	3.533

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.471
r_dihedral_angle_3_deg	15.461
r_dihedral_angle_2_deg	8.476
r_dihedral_angle_1_deg	7.172
r_lrange_it	6.732
r_lrange_other	6.719
r_scangle_it	5.418
r_scangle_other	5.418
r_scbond_it	3.534
r_scbond_other	3.533
r_mcangle_it	3.525
r_mcangle_other	3.525
r_dihedral_angle_other_2_deg	3.472
r_dihedral_angle_other_3_deg	2.873
r_mcbond_it	2.457
r_mcbond_other	2.457
r_angle_refined_deg	1.534
r_angle_other_deg	0.522
r_nbd_refined	0.211
r_nbd_other	0.196
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.179
r_xyhbond_nbd_other	0.169
r_symmetry_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9430
Nucleic Acid Atoms
Solvent Atoms	655
Heterogen Atoms	152

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.