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Human Thrombin in complex with MI341
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% PEG 8000, 20mM sodium phosphate, 175mM sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.9 α = 90 b = 71.1 β = 100.6 c = 72.9 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 mirror 2009-12-12 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 1.78 50 97.9 0.078 14.2 3 32972 32972 13.54
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 1.78 1.81 99.4 0.476 2.1 2.9 1610
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 1.78 34.354 32760 31209 1551 92.76 0.1559 0.1559 0.1544 0.1519 0.1852 0.1819 Random 22.3951
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] 3.9133 -4.2516 -2.1641 -1.7492
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.28 f_angle_d 1.055 f_chiral_restr 0.074 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 314 Heterogen Atoms 68
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling