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Crystal structure of USP7 with RNF169 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 0.2M sodium chloride, 6% w/v PEG 8000, 0.1M Sodium cacodylate, pH 5.8
Crystal Properties Matthews coefficient Solvent content 3.09 60.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.195 α = 90 b = 99.965 β = 95.54 c = 124.299 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 PIXEL DECTRIS PILATUS 6M 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9776 SSRF BL18U1
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 3.1 46.965 99.9 0.115 3.9 3.8 35693
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 3.1 3.15 100 0.679 3.6
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 4WPH 3.11 46.965 33903 1783 99.42 0.228 0.2259 0.2275 0.268 0.2637 RANDOM 78.44
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] 0.01 -0.08 -0.14 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.285 r_dihedral_angle_4_deg 16.901 r_dihedral_angle_3_deg 16.231 r_dihedral_angle_1_deg 6.066 r_mcangle_it 5.252 r_mcbond_it 3.06 r_mcbond_other 3.058 r_angle_refined_deg 1.051 r_angle_other_deg 0.738 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.285 r_dihedral_angle_4_deg 16.901 r_dihedral_angle_3_deg 16.231 r_dihedral_angle_1_deg 6.066 r_mcangle_it 5.252 r_mcbond_it 3.06 r_mcbond_other 3.058 r_angle_refined_deg 1.051 r_angle_other_deg 0.738 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8632 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing