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Crystal structure of the anticoagulant thrombin mutant W215A/E217A bound to PPACK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 18% PEG 8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.11 α = 90 b = 73.83 β = 90 c = 87.33 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 148 IMAGE PLATE RIGAKU RAXIS II mirror 2002-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 30 98.1 13490 13234 34.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 90.6
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 1PPB 2.4 28.31 13463 12594 1299 93.5 0.205 0.205 0.205 0.2127 0.243 0.2494 RANDOM 31.7
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] 0.8 -8.63 7.83
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.6 c_mcangle_it 4.11 c_scangle_it 3.01 c_mcbond_it 2.57 c_scbond_it 1.97 c_improper_angle_d 1.68 c_angle_deg 1.5 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 47
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing