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Crystal Structure of Factor VIIa in complex with 1-[[3-[2-hydroxy-3-(1H-pyrrolo[3,2-c]pyridin-2-yl)phenyl]phenyl]methyl]-3-phenylurea
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 3.75 67.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.217 α = 90 b = 95.217 β = 90 c = 116.197 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 2006-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54190
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 1.98 50 98.4 0.113 7.5 5.4 37285
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 1.98 2.05 87.7 0.716 4.6 3237
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 1.99 24.55 35332 1864 99.1 0.1877 0.186 0.1954 0.2196 0.2228 RANDOM 26.796
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] -0.61 -0.61 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.709 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 13.733 r_dihedral_angle_1_deg 6.701 r_mcangle_it 3.215 r_mcbond_it 1.999 r_mcbond_other 1.999 r_angle_refined_deg 1.718 r_angle_other_deg 0.982 r_chiral_restr 0.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.709 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 13.733 r_dihedral_angle_1_deg 6.701 r_mcangle_it 3.215 r_mcbond_it 1.999 r_mcbond_other 1.999 r_angle_refined_deg 1.718 r_angle_other_deg 0.982 r_chiral_restr 0.261 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 71
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing