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Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 20 mM Sodium dihydrogen phosphate ph 7.5,
350 mM NACl, 27% PEG 8000,
Crystal Properties Matthews coefficient Solvent content 2.5 51.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.367 α = 90 b = 71.49 β = 99.79 c = 72.135 γ = 90
Symmetry Space Group C 1 2 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 Sagitally bended Si111-crystal 2015-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.46 43.13 97.3 0.039 0.999 15.9 2.8 58841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.55 95.3 0.47 2.2 2.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1H8D 1.46 43.13 1.36 58835 2941 97.34 0.1317 0.13 0.133 0.1633 0.1642
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 21.041 f_angle_d 1.217 f_chiral_restr 0.095 f_bond_d 0.012 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data scaling PHASER phasing XDS data reduction