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Human Thrombin in complex with MI328
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 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.5 α = 90 b = 71.3 β = 100.6 c = 72.5 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 105 CCD MARMOSAIC 225 mm CCD Collimating mirror 2009-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
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 1.69 50 97.7 0.059 14.6 2.5 38822 38822 15.82
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 1.69 1.72 98.8 0.49 2 2.4 1961
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 1.69 34.648 38269 36443 1826 92.13 0.1641 0.1641 0.1626 0.161 0.192 0.1908 Random 24.1118
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] 2.044 -2.8331 -1.6085 -0.4355
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.928 f_angle_d 1.06 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 2351 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 71
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling