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Exploring thrombin S3 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, PEG8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.4 α = 90 b = 71.2 β = 100.3 c = 72.2 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 113 IMAGE PLATE RIGAKU RAXIS IV 2008-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.98 50 94 0.042 25.7 3.1 23083 23083 25.2
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 1.98 2.01 72.5 0.207 5.3 2.8 892
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 FOURIER SYNTHESIS FREE R PDB entry 1H8D 1.98 10 22262 19593 1084 91.5 0.178 0.176 0.171 0.1823 0.261 0.2038 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 2 2257 2486.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.081 s_non_zero_chiral_vol 0.043 s_zero_chiral_vol 0.035 s_from_restr_planes 0.0271 s_angle_d 0.024 s_anti_bump_dis_restr 0.014 s_bond_d 0.006 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2300 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 30
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing