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Crystal Structure of Factor VIIa in complex with 1-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-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 3.76 67.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.1 α = 90 b = 95.1 β = 90 c = 116.49 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 2008-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000000 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 1.66 49.67 99.8 0.062 0.069 0.999 14.82 5.54 63461 -3 26.881
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 1.66 1.7 99.5 0.648 0.72 0.798 2.39
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT inhouse model 1.66 49.69 59528 3156 98.04 0.1826 0.182 0.1943 0.2058 RANDOM 20.014
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] -0.42 -0.42 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.077 r_dihedral_angle_4_deg 17.878 r_dihedral_angle_3_deg 14.418 r_dihedral_angle_1_deg 6.285 r_scangle_it 3.03 r_angle_other_deg 2.68 r_scbond_it 1.869 r_angle_refined_deg 1.57 r_mcangle_it 1.453 r_mcbond_it 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.077 r_dihedral_angle_4_deg 17.878 r_dihedral_angle_3_deg 14.418 r_dihedral_angle_1_deg 6.285 r_scangle_it 3.03 r_angle_other_deg 2.68 r_scbond_it 1.869 r_angle_refined_deg 1.57 r_mcangle_it 1.453 r_mcbond_it 0.79 r_mcbond_other 0.15 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2372 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 69
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing