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Crystal structure of active site inhibited coagulation factor VIIA mutant in complex with soluble tissue factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAN PDB ENTRY 1DAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 100mM NaCitrate, 16%(w/v) PEG4000, 12%(v/v) 1-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.06 59.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.361 α = 90 b = 68.558 β = 90.22 c = 78.817 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 80 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.08 MAX II I911-3
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 2.2 29.19 80.3 0.096 1.8 34658 34658 23.5
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 2.2 2.3 26.1 0.229 2.12 1.3 1526
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1DAN 2.2 29.19 34719 32936 1734 100 0.23568 0.23259 0.2425 0.2943 0.2949 RANDOM 33.911
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] -2.13 0.61 -2.32 4.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.327 r_dihedral_angle_4_deg 19.654 r_dihedral_angle_3_deg 18.403 r_dihedral_angle_1_deg 11.67 r_scangle_it 3.171 r_angle_refined_deg 2.17 r_scbond_it 2.124 r_mcangle_it 1.667 r_mcbond_it 0.958 r_symmetry_vdw_refined 0.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.327 r_dihedral_angle_4_deg 19.654 r_dihedral_angle_3_deg 18.403 r_dihedral_angle_1_deg 11.67 r_scangle_it 3.171 r_angle_refined_deg 2.17 r_scbond_it 2.124 r_mcangle_it 1.667 r_mcbond_it 0.958 r_symmetry_vdw_refined 0.526 r_nbtor_refined 0.319 r_symmetry_hbond_refined 0.308 r_nbd_refined 0.275 r_xyhbond_nbd_refined 0.219 r_metal_ion_refined 0.16 r_chiral_restr 0.134 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4119 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 56
Software Software Software Name Purpose MAR345 data collection CCP4 model building MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling CCP4 phasing