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Crystal structure of PCNA in complex with DNA polymerase iota 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 6.4 293 pH6.4, HANGING DROP VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.62 α = 90 b = 68.82 β = 95.05 c = 90.18 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 210 Rhodium coated silicon single crystal mirrors 2007-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 2.3 50 98 0.067 13.5 4.1 44815 -3
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 2.3 2.38 86.4 0.338 3.2 3 4440
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 2.3 19.95 42715 2249 100 0.19627 0.19335 0.2014 0.2512 0.2531 RANDOM 42.506
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] -0.53 0.43 0.4 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.167 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 16.58 r_dihedral_angle_1_deg 7.385 r_angle_other_deg 4.42 r_scangle_it 4.241 r_scbond_it 2.841 r_angle_refined_deg 1.79 r_mcangle_it 1.78 r_mcbond_it 1.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.167 r_dihedral_angle_4_deg 19.853 r_dihedral_angle_3_deg 16.58 r_dihedral_angle_1_deg 7.385 r_angle_other_deg 4.42 r_scangle_it 4.241 r_scbond_it 2.841 r_angle_refined_deg 1.79 r_mcangle_it 1.78 r_mcbond_it 1.533 r_symmetry_vdw_other 0.385 r_symmetry_hbond_refined 0.242 r_nbd_other 0.241 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.211 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.173 r_nbtor_other 0.118 r_chiral_restr 0.105 r_mcbond_other 0.027 r_bond_refined_d 0.02 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 5985 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XDS data scaling MOLREP phasing