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Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% PEG 4000, 0.1M HEPES pH7.0, 0.75M NaCl, 0.04% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 277K, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.46 α = 90 b = 71.64 β = 100.21 c = 71.8 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 100 PIXEL DECTRIS PILATUS 6M 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.979500 Diamond I24
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 1.84 37.86 96.7 2 3.3 26949
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.84 37.86 26949 1434 97.48 0.20054 0.19799 0.2049 0.24775 0.2491 RANDOM 30.563
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] -0.01 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.756 r_dihedral_angle_4_deg 19.446 r_dihedral_angle_3_deg 16.095 r_long_range_B_refined 7.949 r_long_range_B_other 7.947 r_dihedral_angle_1_deg 7.211 r_scangle_other 5.143 r_mcangle_it 3.928 r_mcangle_other 3.927 r_scbond_it 3.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.756 r_dihedral_angle_4_deg 19.446 r_dihedral_angle_3_deg 16.095 r_long_range_B_refined 7.949 r_long_range_B_other 7.947 r_dihedral_angle_1_deg 7.211 r_scangle_other 5.143 r_mcangle_it 3.928 r_mcangle_other 3.927 r_scbond_it 3.465 r_scbond_other 3.464 r_mcbond_it 2.746 r_mcbond_other 2.745 r_angle_refined_deg 2.043 r_angle_other_deg 1.235 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling Sir2014 phasing