☰ Navigation Tabs
Crystal Structure of Human Calpain-3 Protease Core in Complex with E-64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295.15 PEG 8000, MES, calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.01 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.28 α = 90 b = 105.36 β = 90 c = 225.36 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 CCD RAYONIX MX-300 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 30 99.3 0.18 0.99 9.54 4.29 36048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.815 99.7 0.58 0.91 3.29 4.31
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 6BDT 2.8 17.93 34197 1800 99.15 0.2084 0.2055 0.2095 0.2643 0.2578 RANDOM 61.078
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] 4.44 -1.28 -3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.297 r_dihedral_angle_4_deg 13.973 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 6.063 r_angle_refined_deg 1.354 r_angle_other_deg 0.938 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.297 r_dihedral_angle_4_deg 13.973 r_dihedral_angle_3_deg 13.506 r_dihedral_angle_1_deg 6.063 r_angle_refined_deg 1.354 r_angle_other_deg 0.938 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10159 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing