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Crystal structure for the complex of thrombin mutant D102N and hirudin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHH PDB entry 1SHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 20% PEG 3350, 0.2M Ca acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.29 62.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.506 α = 90 b = 89.506 β = 90 c = 133.148 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.2 74.28 95.5 0.07 0.07 23.8 11.5 28265 26993 -0.5 -0.5 39.5
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 2.2 2.24 97.6 0.481 0.481 3.3 7.1 1352
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1SHH 2.2 40 -0.5 -0.5 26781 25485 1348 95.16 0.19996 0.19818 0.1991 0.2335 0.2294 RANDOM 52.611
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] -0.47 -0.47 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.182 r_dihedral_angle_3_deg 18.531 r_dihedral_angle_4_deg 18.206 r_dihedral_angle_1_deg 6.798 r_scangle_it 2.877 r_scbond_it 1.771 r_angle_refined_deg 1.463 r_mcangle_it 0.923 r_mcbond_it 0.487 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.182 r_dihedral_angle_3_deg 18.531 r_dihedral_angle_4_deg 18.206 r_dihedral_angle_1_deg 6.798 r_scangle_it 2.877 r_scbond_it 1.771 r_angle_refined_deg 1.463 r_mcangle_it 0.923 r_mcbond_it 0.487 r_chiral_restr 0.105 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2802 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 27
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling