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Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 143
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y5L 4Y5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 290 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 143 with the SMILES code CC1=CSC(=O)N1CCCC(=O)NC1=NC=CS1
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.23 α = 90 b = 72.88 β = 109.2 c = 52.72 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 CCD MAR CCD 165 mm 2014-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.3 0.8944 BESSY 14.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.35 17.64 97.7 0.07 0.07 0.08 0.039 11.1 4.1 69212 69212 10.74
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 95 0.451 0.451 0.519 0.255 1.7 3.9 9813
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 THROUGHOUT 4Y5L 1.35 17.575 1.34 69203 3510 97.78 0.1383 0.1371 0.1383 0.1615 0.1623 RANDOM 14.0703
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 10.608 f_angle_d 1.184 f_chiral_restr 0.071 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing PDB_EXTRACT data extraction iMOSFLM data reduction SCALA data scaling