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Crystal Structure of Factor VIIa in complex with 5-hydroxy-N-(3-oxo-1,2-dihydroisoindol-5-yl)-1-[3-[(phenylcarbamoylamino)methyl]phenyl]pyrazole-4-carboxamide
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 3.77 67.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.28 α = 90 b = 95.28 β = 90 c = 116.57 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 2008-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.979000 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 1.62 36.89 99.8 0.059 0.063 0.999 20.56 7.2 68291 -3 25.257
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 1.62 1.66 98.2 0.61 0.661 0.874 3.53
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 1.62 36.89 63575 3371 97.91 0.1623 0.1614 0.1746 0.179 0.1906 RANDOM 23.252
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 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.017 r_dihedral_angle_4_deg 21.726 r_dihedral_angle_3_deg 12.095 r_dihedral_angle_1_deg 6.281 r_mcangle_it 3.437 r_mcbond_it 2.28 r_mcbond_other 2.277 r_angle_refined_deg 2.059 r_angle_other_deg 1.059 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.017 r_dihedral_angle_4_deg 21.726 r_dihedral_angle_3_deg 12.095 r_dihedral_angle_1_deg 6.281 r_mcangle_it 3.437 r_mcbond_it 2.28 r_mcbond_other 2.277 r_angle_refined_deg 2.059 r_angle_other_deg 1.059 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2350 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 65
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing