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High affinity inhibitor of human thrombin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H8D PDB ENTRY 1H8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 PHOSPHATE BUFFER, SODIUM CHLORIDE, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.77 α = 90 b = 71.35 β = 100.65 c = 72.39 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 110 CCD MAR CCD 165 mm 2008-05-03 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 1.55 30 92.7 0.046 17 2.5 47623 47623
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 1.55 1.58 96.5 0.323 2.6 2.4 2488
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING FREE R PDB ENTRY 1H8D 1.55 10 43173 47623 2275 84.3 0.2436 0.217 0.209 0.271 0.2548 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 4 2493
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.082 s_non_zero_chiral_vol 0.06 s_zero_chiral_vol 0.049 s_angle_d 0.027 s_from_restr_planes 0.0265 s_anti_bump_dis_restr 0.013 s_bond_d 0.009 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2282 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 49
Software Software Software Name Purpose HKL-2000 data collection SHELX model building SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing