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human factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-1-[3-[[(3,5-dimethyl-1,2-oxazol-4-yl)carbamoylamino]methyl]phenyl]-5-hydroxypyrazole-4-carboxamide at 1.73A
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 = 95.39 α = 90 b = 95.39 β = 90 c = 116.32 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 2008-10-03 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 1.73 36.88 99.7 0.059 0.064 0.999 18.87 7.12 56045 -3 25.415
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 1.73 1.78 97.5 0.3 0.324 0.957 6.05
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 1.73 36.89 53110 2836 99.65 0.1647 0.1638 0.1754 0.1815 0.1937 RANDOM 19.972
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] -0.26 -0.26 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.606 r_dihedral_angle_4_deg 20.659 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 6.045 r_scangle_it 4.283 r_scbond_it 2.603 r_mcangle_it 1.902 r_angle_refined_deg 1.589 r_mcbond_it 1.061 r_angle_other_deg 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.606 r_dihedral_angle_4_deg 20.659 r_dihedral_angle_3_deg 13.56 r_dihedral_angle_1_deg 6.045 r_scangle_it 4.283 r_scbond_it 2.603 r_mcangle_it 1.902 r_angle_refined_deg 1.589 r_mcbond_it 1.061 r_angle_other_deg 0.941 r_mcbond_other 0.274 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2350 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 55
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing