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Crystal Structure of Factor VIIa in complex with N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]pentanamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other inhouse model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 3.76 67.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.157 α = 90 b = 95.157 β = 90 c = 116.458 γ = 90
Symmetry Space Group P 41 21 2
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 MAR scanner 345 mm plate 2008-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 30.6 99.8 0.034 0.034 16.87 1.88 46257
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 99.2 0.228 0.228 2.6 1.88
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 inhouse model 1.9 30.1 40575 2169 99.94 0.1888 0.1876 0.1966 0.2105 0.2175 RANDOM 21.801
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] -0.26 -0.26 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.163 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.021 r_angle_other_deg 2.667 r_scangle_it 2.13 r_angle_refined_deg 1.527 r_scbond_it 1.232 r_mcangle_it 1.05 r_mcbond_it 0.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.163 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.021 r_angle_other_deg 2.667 r_scangle_it 2.13 r_angle_refined_deg 1.527 r_scbond_it 1.232 r_mcangle_it 1.05 r_mcbond_it 0.561 r_mcbond_other 0.073 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SADABS data scaling PHASER phasing