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human factor VIIa in complex with 1-[[3-[5-hydroxy-3-methyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]-3-phenylurea at 2.43A
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 3.81 67.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.345 α = 90 b = 95.345 β = 90 c = 117.608 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 2008-06-06 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 2.43 47.67 99.7 0.132 0.132 19.26 15.36 21062
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 2.43 2.52 98 0.61 0.61 3.29 12.2
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 2.43 47.67 19914 1009 99.34 0.2013 0.1998 0.2081 0.2298 0.2341 RANDOM 39.13
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] -0.48 -0.48 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 19.476 r_dihedral_angle_3_deg 16.61 r_dihedral_angle_1_deg 6.892 r_angle_other_deg 2.814 r_scangle_it 2.54 r_angle_refined_deg 1.762 r_scbond_it 1.527 r_mcangle_it 1.237 r_mcbond_it 0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 19.476 r_dihedral_angle_3_deg 16.61 r_dihedral_angle_1_deg 6.892 r_angle_other_deg 2.814 r_scangle_it 2.54 r_angle_refined_deg 1.762 r_scbond_it 1.527 r_mcangle_it 1.237 r_mcbond_it 0.647 r_mcbond_other 0.083 r_chiral_restr 0.073 r_bond_refined_d 0.013 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 2350 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SADABS data scaling PHASER phasing