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Crystal structure of human PCNA soaked with p47phox(106-127) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 19 to 23% PEG 3350, 0.2 to 0.3 M NaCl, 0.1 M Tris-HCl pH 8.5
12h prior to crystal freezing, 100 uM of p47phox(106-127) peptide was added to the crystallization drop
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.88 α = 90 b = 140.67 β = 90 c = 171.77 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2016-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96600 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.22 41 99.4 0.096 0.106 0.999 14.3 5.71 16369
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.22 3.3 97.8 1.71 1.88 0.59 5.61
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 1AXC 3.22 41 14362 733 91.62 0.21206 0.2089 0.2112 0.27178 0.2678 RANDOM 118.148
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] 0.15 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.814 r_dihedral_angle_3_deg 16.483 r_dihedral_angle_4_deg 13.856 r_long_range_B_refined 13.532 r_long_range_B_other 13.532 r_mcangle_it 9.537 r_mcangle_other 9.536 r_scangle_other 9.317 r_dihedral_angle_1_deg 6.655 r_mcbond_it 5.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.814 r_dihedral_angle_3_deg 16.483 r_dihedral_angle_4_deg 13.856 r_long_range_B_refined 13.532 r_long_range_B_other 13.532 r_mcangle_it 9.537 r_mcangle_other 9.536 r_scangle_other 9.317 r_dihedral_angle_1_deg 6.655 r_mcbond_it 5.926 r_mcbond_other 5.921 r_scbond_it 5.729 r_scbond_other 5.727 r_angle_refined_deg 1.233 r_angle_other_deg 0.855 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5777 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing