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Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]-3-phenylpropanamide
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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.03 α = 90 b = 95.03 β = 90 c = 116.84 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 0.984000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.48 39.94 99.8 0.07 0.074 0.999 16.68 8.94 88673 -3 24.924
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.52 98.3 1.23 1.332 0.526 1.49
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 1.48 39.94 83985 4440 99.57 0.2001 0.1998 0.2068 0.2063 0.2154 RANDOM 16.39
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] -0.13 -0.13 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.98 r_dihedral_angle_4_deg 18.02 r_dihedral_angle_3_deg 14.918 r_dihedral_angle_1_deg 6.008 r_angle_other_deg 2.628 r_scangle_it 1.825 r_angle_refined_deg 1.472 r_scbond_it 1.09 r_mcangle_it 0.952 r_mcbond_it 0.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.98 r_dihedral_angle_4_deg 18.02 r_dihedral_angle_3_deg 14.918 r_dihedral_angle_1_deg 6.008 r_angle_other_deg 2.628 r_scangle_it 1.825 r_angle_refined_deg 1.472 r_scbond_it 1.09 r_mcangle_it 0.952 r_mcbond_it 0.507 r_chiral_restr 0.064 r_mcbond_other 0.06 r_bond_refined_d 0.009 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 381 Heterogen Atoms 59
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing