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human factor VIIa in complex with 1-[[3-[5-hydroxy-4-(7H-pyrrolo[2,3-d]pyrimidin-6-yl)pyrazol-1-yl]phenyl]methyl]-3-phenylurea at 1.84A
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
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.037 α = 90 b = 95.037 β = 90 c = 116.512 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 IMAGE PLATE MAR scanner 345 mm plate 2008-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54177
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 1.84 49.67 98.5 0.063 0.063 22.22 9.57 46187
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 1.84 1.94 90.1 0.363 0.363 4.5 7.07
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 1.84 47.51 43544 2320 98 0.186 0.1853 0.1942 0.1998 0.2102 RANDOM 23.166
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] -0.38 -0.38 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.585 r_dihedral_angle_4_deg 16.859 r_dihedral_angle_3_deg 13.883 r_dihedral_angle_1_deg 6.466 r_scangle_it 2.85 r_angle_other_deg 2.055 r_scbond_it 1.662 r_angle_refined_deg 1.427 r_mcangle_it 1.303 r_mcbond_it 0.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.585 r_dihedral_angle_4_deg 16.859 r_dihedral_angle_3_deg 13.883 r_dihedral_angle_1_deg 6.466 r_scangle_it 2.85 r_angle_other_deg 2.055 r_scbond_it 1.662 r_angle_refined_deg 1.427 r_mcangle_it 1.303 r_mcbond_it 0.693 r_mcbond_other 0.119 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SADABS data scaling PHASER phasing