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The structure of Schizosaccharomyces pombe PCNA in complex with an Spd1 derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 295 100 mM TRIS-HCl pH 7.5, 18% (w/v) PEG4000 and 6% (v/v) glycerol, in the presence of 1.9 mM Spd1(27-46).
[PCNA]=0.17 mM (5 mg/mL)
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.86 α = 90 b = 71.65 β = 115.75 c = 84.02 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 PILATUS 6M 2015-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.9 75.7 99.1 0.991 6.5 4.1 19183 39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 99.2 0.552 0.096 1.5 4.3
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 3WGW 2.9 75.68 18195 980 98.9 0.2356 0.23415 0.2345 0.2615 0.2587 RANDOM
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] 0.71 1.32 0.23 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.908 r_dihedral_angle_3_deg 18.653 r_dihedral_angle_4_deg 17.736 r_long_range_B_refined 16.998 r_long_range_B_other 16.998 r_scangle_other 11.388 r_mcangle_it 8.535 r_mcangle_other 8.535 r_dihedral_angle_1_deg 6.947 r_scbond_it 6.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.908 r_dihedral_angle_3_deg 18.653 r_dihedral_angle_4_deg 17.736 r_long_range_B_refined 16.998 r_long_range_B_other 16.998 r_scangle_other 11.388 r_mcangle_it 8.535 r_mcangle_other 8.535 r_dihedral_angle_1_deg 6.947 r_scbond_it 6.896 r_scbond_other 6.895 r_mcbond_it 5.249 r_mcbond_other 5.244 r_angle_refined_deg 1.889 r_angle_other_deg 1.878 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 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 5797 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing