☰ Navigation Tabs
Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic 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, HANGING 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 2.74 55.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.72 α = 90 b = 78.43 β = 91.12 c = 56.3 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 6M 2013-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.64 41.99 97.5 0.052 0.031 0.997 16.1 3.7 51550 51550
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 1.64 1.68 96.5 0.901 0.547 0.666 1.7 3.6 3749
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 1.64 41.99 48906 2620 97.33 0.1713 0.1699 0.18 0.1966 0.1738 RANDOM 34.082
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] -0.14 -0.38 1.07 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.424 r_dihedral_angle_4_deg 21.246 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_1_deg 5.192 r_mcangle_it 3.058 r_mcbond_it 2.203 r_mcbond_other 2.203 r_angle_refined_deg 1.967 r_angle_other_deg 1.004 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.424 r_dihedral_angle_4_deg 21.246 r_dihedral_angle_3_deg 15.979 r_dihedral_angle_1_deg 5.192 r_mcangle_it 3.058 r_mcbond_it 2.203 r_mcbond_other 2.203 r_angle_refined_deg 1.967 r_angle_other_deg 1.004 r_chiral_restr 0.142 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 157 Heterogen Atoms 56
Software Software Software Name Purpose Aimless data scaling Coot model building REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction PHASER phasing