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Crystal Structure of Human Protein Phosphatase 5C (PP5C) in complex with a triazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 20-26% MPD, 4-8% PEG5000MME, 1 mM Manganese chloride, 10 mM Tris
Crystal Properties Matthews coefficient Solvent content 1.98 37.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.805 α = 87.99 b = 80.708 β = 87.1 c = 91.384 γ = 86.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2014-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.96 91.22 97.5 0.161 0.161 5.6 2 81256
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 96.2 0.481 0.481 1.8 2
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 1S95 1.96 91.22 77174 4073 97.46 0.2129 0.21115 0.2152 0.24565 0.2481 RANDOM 23.135
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.858 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_4_deg 12.108 r_dihedral_angle_1_deg 6.437 r_long_range_B_refined 2.922 r_long_range_B_other 2.915 r_mcangle_it 1.536 r_mcangle_other 1.536 r_scangle_other 1.521 r_angle_refined_deg 1.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.858 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_4_deg 12.108 r_dihedral_angle_1_deg 6.437 r_long_range_B_refined 2.922 r_long_range_B_other 2.915 r_mcangle_it 1.536 r_mcangle_other 1.536 r_scangle_other 1.521 r_angle_refined_deg 1.187 r_angle_other_deg 0.903 r_mcbond_it 0.884 r_mcbond_other 0.884 r_scbond_it 0.872 r_scbond_other 0.871 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 10059 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing