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Crystal structure of human prothrombin mutant S101C/A470C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EDM 5EDM and 3NXP experimental model PDB 3NXP 5EDM and 3NXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 277 100 mM Bicine, pH 9.0 and 11% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.03 α = 105.35 b = 85.074 β = 90 c = 153.801 γ = 90.05
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++ 2017-11-17 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 4.1 40 91.7 0.156 5.7 2.5 30018 -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 4.1 4.17 74.1 0.675 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5EDM and 3NXP 4.12 30.32 26884 1394 88.04 0.28085 0.27826 0.2889 0.33298 0.3226 RANDOM 191.324
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] 33.56 -6.84 51.31 20.54 14.49 -54.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.082 r_long_range_B_refined 21.73 r_long_range_B_other 21.729 r_dihedral_angle_3_deg 15.765 r_mcangle_it 14.908 r_mcangle_other 14.907 r_scangle_other 11.479 r_dihedral_angle_4_deg 10.358 r_mcbond_it 8.852 r_mcbond_other 8.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.082 r_long_range_B_refined 21.73 r_long_range_B_other 21.729 r_dihedral_angle_3_deg 15.765 r_mcangle_it 14.908 r_mcangle_other 14.907 r_scangle_other 11.479 r_dihedral_angle_4_deg 10.358 r_mcbond_it 8.852 r_mcbond_other 8.848 r_dihedral_angle_1_deg 6.673 r_scbond_it 6.628 r_scbond_other 6.62 r_angle_refined_deg 1.177 r_angle_other_deg 0.917 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 9188 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing