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Structure of a proline specific mutant of human cathepsin L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 PEG 4000, 2-propanol
Crystal Properties Matthews coefficient Solvent content 1.8 31.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.22 α = 90 b = 67.584 β = 90 c = 103.239 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 MAR CCD 165 mm 2016-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 1.0 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.457 50 94.4 0.084 0.092 0.035 14.3 6.3 49550 17.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.49 63.6 0.386 0.427 0.18 0.91 4.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CS8 1.457 25.561 1.33 49436 1996 94.31 0.1934 0.1916 0.2369 0.2478 31.3457
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 17.973 f_angle_d 1.12 f_chiral_restr 0.184 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2508 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 171
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing