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Crystal structure of Thrombin in complex with a Chlorothiophene-based inhibitor, CP3, discovered by a novel rapid nanoscale library screening.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T7H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Sodium-HEPES, 100 mM MOPS pH 7.5, 100 mM amino acids (20 mM D-L
glutamic acid monohydrate, 20mM D-L alanine, 20 mM glycine, 20mM D-L lysine
monohydrochloride, 20mM D-L serine) 12,5% v/v MPD;
12,5% w/v PEG1000,
12,5% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.931 α = 90 b = 98.26 β = 90 c = 145.661 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 9M 2024-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8371 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.1 66.74 87.7 0.973 2.1 3.1 10601
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.31 96.4 0.999 0.495 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.1 66.74 1.34 10580 494 86.4 0.2642 0.2632 0.2634 0.2844 0.2845 72
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.8645 f_angle_d 0.7361 f_chiral_restr 0.0768 f_plane_restr 0.0049 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4636 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing