9Y62 | pdb_00009y62

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RBH	Human DNA polymerase beta crosslinked ternary complex 2

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	0.1 M Sodium Citrate pH 5.5, 18% PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2	45.23

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 PILATUS3 S 6M		2025-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	2.1	45.92	90.8	0.09	1	9.6	3.8		20468

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	2.1	2.16			0.09	1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	45.92	20466	1099	90.574	0.207	0.2041	0.2045	0.2566	0.2573	RANDOM	59.513

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]
0.106		-0.008	0.061		-0.141

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.452
r_dihedral_angle_6_deg	14.701
r_lrange_it	10.619
r_dihedral_angle_2_deg	9.739
r_scangle_it	8.881
r_mcangle_it	7.079
r_dihedral_angle_1_deg	6.727
r_scbond_it	6.135
r_mcbond_it	4.878
r_angle_refined_deg	1.682

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.452
r_dihedral_angle_6_deg	14.701
r_lrange_it	10.619
r_dihedral_angle_2_deg	9.739
r_scangle_it	8.881
r_mcangle_it	7.079
r_dihedral_angle_1_deg	6.727
r_scbond_it	6.135
r_mcbond_it	4.878
r_angle_refined_deg	1.682
r_nbtor_refined	0.314
r_nbd_refined	0.237
r_metal_ion_refined	0.195
r_symmetry_nbd_refined	0.174
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.109
r_symmetry_xyhbond_nbd_refined	0.106
r_gen_planes_refined	0.007
r_bond_refined_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2438
Nucleic Acid Atoms	631
Solvent Atoms	28
Heterogen Atoms	46

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.