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Calpain-5 (CAPN5) Protease Core (PC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other SAXS guided homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 250 mM sodium phosphate, 12 % PEG 8000, 36 mM EDTA, 10 mM Calcium chloride, 0.4 mM H-E(EDANS)-KIEIVRKKPIFKKATV-K(DASBCYL)-OH
Crystal Properties Matthews coefficient Solvent content 2.71 54.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.038 α = 90 b = 51.576 β = 110.425 c = 110.635 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 CMOS RDI CMOS_8M 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2
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 51.84 99.44 0.087 0.996 10.8 2 22239 50.65
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 2.9 99.07 0.623 0.804 1.73 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE SAXS guided homology model 2.8 51.84 1.34 22202 1060 99.48 0.2295 0.2268 0.2289 0.2851 0.2897 RANDOM 50.18
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 f_dihedral_angle_d 11.4344 f_angle_d 1.1199 f_chiral_restr 0.0593 f_bond_d 0.0097 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5595 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction Aimless data scaling Coot model building PHASER phasing