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1.9 angstrom crystal structure of wild-type human thrombin in the sodium free state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPB PDB entry 1PPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 PEG 3350, magnesium acetate, lithium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.34 α = 90 b = 82.31 β = 90 c = 50.93 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 4 Rh coated Si mirror 2005-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.8700 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.93 50.9 99.9 0.11 0.103 14.6 8.2 49378 49378 2 17.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.03 99.4 0.55 0.55 1.1 6.8 7065
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 THROUGHOUT PDB entry 1PPB 1.93 19.97 49332 49279 1513 99.8 0.203 0.198 0.197 0.2152 0.229 0.2495 RANDOM 26.9
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] 2.7 -2.62 -0.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_scangle_it 3.03 c_mcangle_it 2.24 c_scbond_it 2.02 c_angle_deg 1.4 c_mcbond_it 1.37 c_improper_angle_d 0.81 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4326 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 42
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing ARP/wARP model building CNS refinement CCP4 data scaling