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Thrombin Inhibition by Pyridin Derivatives
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 7.5 277.15 15% PEG8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.2 α = 90 b = 71.1 β = 100.6 c = 72.8 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 CCD RAYONIX MX-225 Collimating mirrors 2009-04-21 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 Sym I (Observed) 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 30 96 0.048 22.3 3 74225 74225 10.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 71.2 0.293 2.8 2 2719
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Free R 1H8D 1.35 24.758 75310 71675 3635 93.01 0.1328 0.1328 0.1315 0.1275 0.1559 0.152 Random 19.4443
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] 1.1776 -0.4833 -0.6876 -0.49
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.154 f_angle_d 1.127 f_chiral_restr 0.078 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2341 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 55
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling