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Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 116
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 116 with the SMILES code OC(=O)C1=CC=CC=C1SC[C@H]1CCCO1
Crystal Properties Matthews coefficient Solvent content 2.44 49.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.319 α = 90 b = 73.102 β = 109.48 c = 52.796 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 MARMOSAIC 225 mm CCD 2014-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.2 42.726 98.8 0.056 0.065 0.999 15.8 4.107 101126 -3 9.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.27 93.9 0.575 0.671 0.73 2.32
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 1.196 36.551 1.36 101123 5056 98.92 0.1346 0.1339 0.1357 0.1484 0.1496 RANDOM 12.7911
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 10.605 f_angle_d 1.183 f_chiral_restr 0.071 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling PHENIX refinement PHASER phasing PDB_EXTRACT data extraction XDS data reduction