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High resolution crystal structure of human PSMD10 (Gankyrin)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UOH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 60% v/v Tacsimate pH 7.0 (Hampton Research)
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.085 α = 90 b = 60.085 β = 90 c = 122.377 γ = 120
Symmetry Space Group P 32 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 80 CCD MARMOSAIC 225 mm CCD 2020-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9795 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.55 47.93 99 0.108 0.035 7.1 8.8 37545 16.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 86.2 2.693 1.217 0.1 4.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UOH 1.71 47.93 26844 1505 99.79 0.198 0.1961 0.2314 0.1866 RANDOM 26.382
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.662 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_4_deg 7.784 r_dihedral_angle_1_deg 5.678 r_angle_other_deg 1.831 r_angle_refined_deg 1.613 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.662 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_4_deg 7.784 r_dihedral_angle_1_deg 5.678 r_angle_other_deg 1.831 r_angle_refined_deg 1.613 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1693 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction