☰ Navigation Tabs
Human DNA polymerase beta crosslinked ternary complex 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M Citrate pH 5.5, 18% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.36 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.51 α = 90 b = 78.43 β = 113.22 c = 57.19 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2016-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection 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 1.9 52.56 91.5 0.074 0.087 0.045 0.996 12 3.5 32605
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 1.9 1.94 88.3 0.385 0.459 0.247 0.581 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4KLD 1.9 51.07 30989 1614 91.64 0.1811 0.1789 0.2225 0.213 RANDOM 21.27
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] -0.01 0.01 0.06 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.17 r_dihedral_angle_4_deg 15.884 r_dihedral_angle_3_deg 15.213 r_dihedral_angle_1_deg 5.991 r_angle_refined_deg 1.483 r_angle_other_deg 1.357 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.17 r_dihedral_angle_4_deg 15.884 r_dihedral_angle_3_deg 15.213 r_dihedral_angle_1_deg 5.991 r_angle_refined_deg 1.483 r_angle_other_deg 1.357 r_chiral_restr 0.088 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 2567 Nucleic Acid Atoms 628 Solvent Atoms 266 Heterogen Atoms 59
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing