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Exploring Thrombin S1 Pocket
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 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70 α = 90 b = 70.3 β = 101.1 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 110 CCD MAR CCD 165 mm Si [111], horizontally focussing 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.80150 EMBL/DESY, HAMBURG X13
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 2.2 50 91.2 0.046 18.7 2.9 16506 16506
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 2.2 2.25 69.1 0.166 6.06 2.5 819
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 AB INITIO PHASING FREE R PDB entry 1H8D 2.2 10 15874 15874 775 88.6 0.1735 0.1702 0.1702 0.1696 0.2669 0.1922 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 2546
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.083 s_non_zero_chiral_vol 0.037 s_zero_chiral_vol 0.029 s_from_restr_planes 0.0253 s_angle_d 0.021 s_anti_bump_dis_restr 0.007 s_bond_d 0.005 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2341 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 29
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHELX phasing