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Human calpain PEF(S) with (2Z,2Z')-2,2'-disulfanediylbis(3-(6-bromoindol-3-yl)acrylic acid) bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 3 UL PROTEIN (10 MG/ML PEF(S), 5 MM SODIUM CACODYLATE, 2 MM EDTA, 5 MM BME, 1 MM CALCIUM CHLORIDE, PH 7.0) + 3 UL PRECIPITANT (50 MM SODIUM CACODYLATE, 12.5% PEG6000, 20 MM CALCIUM CHLORIDE, PH 7.0) + 1 UL WATER
Crystal Properties Matthews coefficient Solvent content 2.8 56.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.56 α = 90 b = 79.31 β = 91.47 c = 57.02 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 2M 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.79 39.65 97.6 0.071 0.043 0.994 11 3.7 40565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.84 99.8 0.634 0.368 0.744 2 3.9 3101
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 4phj 1.79 39.65 38513 2031 97.49 0.1795 0.1776 0.1876 0.2149 0.2206 RANDOM 29.752
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] -0.04 -0.76 0.62 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.992 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_1_deg 5.959 r_mcangle_it 2.551 r_angle_refined_deg 2.024 r_mcbond_it 1.8 r_mcbond_other 1.799 r_angle_other_deg 1.016 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.992 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_1_deg 5.959 r_mcangle_it 2.551 r_angle_refined_deg 2.024 r_mcbond_it 1.8 r_mcbond_other 1.799 r_angle_other_deg 1.016 r_chiral_restr 0.135 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 136
Software Software Software Name Purpose Aimless data scaling Coot model building REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction PHASER phasing