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Crystal Structure of Factor VIIa in complex with 1-[[3-[4-(5-amino-1H-pyrrolo[3,2-b]pyridin-2-yl)-5-hydroxypyrazol-1-yl]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 67.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.192 α = 90 b = 95.192 β = 90 c = 116.08 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 CCD MARMOSAIC 225 mm CCD 2008-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98399 SLS X10SA
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 1.9 49.56 98.6 0.124 0.124 10.71 8.69 42139
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 1.9 2 90.9 0.493 0.493 1.89 3.13
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 47.62 39463 2091 97.42 0.1921 0.1911 0.1972 0.2112 0.2189 RANDOM 23.534
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] -0.46 -0.46 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.471 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 14.375 r_dihedral_angle_1_deg 5.863 r_angle_other_deg 2.636 r_scangle_it 2.259 r_angle_refined_deg 1.482 r_scbond_it 1.309 r_mcangle_it 1.128 r_mcbond_it 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.471 r_dihedral_angle_4_deg 17.653 r_dihedral_angle_3_deg 14.375 r_dihedral_angle_1_deg 5.863 r_angle_other_deg 2.636 r_scangle_it 2.259 r_angle_refined_deg 1.482 r_scbond_it 1.309 r_mcangle_it 1.128 r_mcbond_it 0.603 r_mcbond_other 0.079 r_chiral_restr 0.066 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 2376 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SADABS data scaling PHASER phasing