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Structure of prethrombin-2 mutant s195a bound to the active site inhibitor argatroban
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 100 mM TRIS PH 8.5, 200 mM LI2SO4 AND 30% PEG 3000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.919 α = 90 b = 81.84 β = 100.62 c = 77.761 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2012-04-22 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) 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 32.13 94.6 0.156 5.9 3.5 11154 10552 -1 -1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 89.8 0.447 2 2.4 493
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 3SQH 3 32.13 -1 -1 10427 9833 477 94.3 0.252 0.248 0.2489 0.343 0.3379 RANDOM 30.03
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] -0.07 -0.01 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.181 r_dihedral_angle_3_deg 20.336 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_1_deg 5.79 r_angle_refined_deg 1.105 r_scangle_it 0.876 r_mcangle_it 0.508 r_scbond_it 0.499 r_mcbond_it 0.273 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.181 r_dihedral_angle_3_deg 20.336 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_1_deg 5.79 r_angle_refined_deg 1.105 r_scangle_it 0.876 r_mcangle_it 0.508 r_scbond_it 0.499 r_mcbond_it 0.273 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4610 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 70
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling