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Crystal structure of active site inhibited coagulation factor VIIA 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 0.1 M sodium citrate, pH 5.6, 16.0 % (w/v) PEG 4000, 12 % (v/v) 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.41 63.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.312 α = 90 b = 68.827 β = 90.74 c = 78.732 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 CCD 2005-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.05 SLS X06SA
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 2.05 39.15 99.6 0.132 8 4.2 52511 52511
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 2.05 2.1 98.9 0.69 2.26 4.1 3582
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 (All) 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 2.05 39.15 52510 52510 2626 100 0.231 0.231 0.228 0.2294 0.273 0.2716 RANDOM 39.466
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] -3.14 0.69 -1.45 4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.609 r_dihedral_angle_3_deg 17.341 r_dihedral_angle_4_deg 16.084 r_dihedral_angle_1_deg 15.64 r_mcangle_it 3.894 r_scangle_it 3.719 r_mcbond_it 2.759 r_scbond_it 2.72 r_angle_refined_deg 2.495 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.609 r_dihedral_angle_3_deg 17.341 r_dihedral_angle_4_deg 16.084 r_dihedral_angle_1_deg 15.64 r_mcangle_it 3.894 r_scangle_it 3.719 r_mcbond_it 2.759 r_scbond_it 2.72 r_angle_refined_deg 2.495 r_nbtor_refined 0.338 r_nbd_refined 0.289 r_symmetry_vdw_refined 0.263 r_xyhbond_nbd_refined 0.262 r_symmetry_hbond_refined 0.208 r_chiral_restr 0.194 r_metal_ion_refined 0.055 r_bond_refined_d 0.028 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4097 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction PHASER phasing