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Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 247
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 247 with the SMILES code CC1=CC=C(C=C1)C(=O)NCC1=NN=C2C=CC=CN12
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.332 α = 90 b = 73.095 β = 109.39 c = 52.731 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 2013-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 1.18 42.761 95.3 0.054 0.064 0.998 12.63 3.567 101460 -3 9.06
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 1.18 1.25 75 0.28 0.351 0.876 2.85
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 1.18 42.761 2 101459 5073 95.35 0.1246 0.124 0.1252 0.1366 0.1382 RANDOM 12.1463
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 10.743 f_angle_d 1.218 f_chiral_restr 0.071 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms
Software Software Software Name Purpose XDS data scaling PHENIX refinement PHASER phasing PDB_EXTRACT data extraction XDS data reduction