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Modulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% polyethylene glycol 3350
0.1 M sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.34 47.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.993 α = 90 b = 42.3 β = 102.7 c = 141.827 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 PIXEL DECTRIS PILATUS3 S 6M 2016-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1 ESRF ID29
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 3.2 46.12 95.3 0.105 5.7 2.2 14271
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 3.2 3.37 98.8 0.32 2.2 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 4D2G 3.2 40.48 13440 716 94.23 0.26401 0.26063 0.2588 0.32715 0.3319 RANDOM 63.479
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] 5.01 3.76 0.27 -6.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.545 r_dihedral_angle_3_deg 19.602 r_dihedral_angle_4_deg 12.614 r_dihedral_angle_1_deg 7.672 r_long_range_B_refined 4.507 r_long_range_B_other 4.506 r_scangle_other 2.806 r_scbond_it 1.654 r_scbond_other 1.654 r_mcangle_it 1.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.545 r_dihedral_angle_3_deg 19.602 r_dihedral_angle_4_deg 12.614 r_dihedral_angle_1_deg 7.672 r_long_range_B_refined 4.507 r_long_range_B_other 4.506 r_scangle_other 2.806 r_scbond_it 1.654 r_scbond_other 1.654 r_mcangle_it 1.652 r_mcangle_other 1.652 r_angle_refined_deg 1.396 r_angle_other_deg 1.021 r_mcbond_it 0.964 r_mcbond_other 0.964 r_chiral_restr 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5506 Nucleic Acid Atoms 410 Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing