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Crystal structure of PCNA in complex with DNA polymerase kappa fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYM PDB ENTRY 1VYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 HANGING DROP VAPOR DIFFUSION 5.2 293 pH5.2, HANGING DROP VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.769 α = 87.25 b = 74.707 β = 77.46 c = 109.049 γ = 80.26
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 RIGAKU MSC JUPITER 210 mirrors 2006-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 50 90.6 0.082 9.1 2.7 71006 -3 53
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 90.6 0.241 4.1 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VYM 2.5 20 67254 3575 100 0.22865 0.22542 0.2236 0.28943 0.2777 RANDOM 37.715
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] -1.04 -0.1 0.45 -0.12 0.19 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.488 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 19.307 r_dihedral_angle_1_deg 6.9 r_scangle_it 5.402 r_scbond_it 3.484 r_mcangle_it 2.305 r_angle_refined_deg 1.872 r_mcbond_it 1.317 r_angle_other_deg 1.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.488 r_dihedral_angle_4_deg 19.537 r_dihedral_angle_3_deg 19.307 r_dihedral_angle_1_deg 6.9 r_scangle_it 5.402 r_scbond_it 3.484 r_mcangle_it 2.305 r_angle_refined_deg 1.872 r_mcbond_it 1.317 r_angle_other_deg 1.235 r_mcbond_other 0.349 r_chiral_restr 0.101 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11928 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing