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Thrombin in complex with MI2100 ((S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-L-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 2.47 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.84 α = 90 b = 71.119 β = 100.58 c = 72.858 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 IMAGE PLATE MAR scanner 345 mm plate Sagitally bended Si111 crystal 2017-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.45 43.431 99 0.045 1 15.41 3.4 61523
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.54 97.9 0.5 0.81 2.34 3.5
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 1.45 21.784 1.37 61497 3075 99.02 0.1335 0.1318 0.1342 0.1645 0.1666
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 22.171 f_angle_d 0.995 f_chiral_restr 0.081 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2302 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data scaling PHASER phasing XDS data reduction