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Crystal Structure of Factor VIIa in complex with isoquinoline-1,6-diamine
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 = 95.195 α = 90 b = 95.195 β = 90 c = 116.759 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 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 99.6 0.154 5.3 4.3 27882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 97.6 0.882 3.1 2672
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 2.2 47.62 23673 1247 89.2 0.1858 0.1841 0.1955 0.2199 0.2214 RANDOM 34.438
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] -0.43 -0.43 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.315 r_dihedral_angle_4_deg 19.433 r_dihedral_angle_3_deg 15.559 r_dihedral_angle_1_deg 6.788 r_scangle_it 2.984 r_scbond_it 1.926 r_mcangle_it 1.476 r_angle_refined_deg 1.452 r_angle_other_deg 0.917 r_mcbond_it 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.315 r_dihedral_angle_4_deg 19.433 r_dihedral_angle_3_deg 15.559 r_dihedral_angle_1_deg 6.788 r_scangle_it 2.984 r_scbond_it 1.926 r_mcangle_it 1.476 r_angle_refined_deg 1.452 r_angle_other_deg 0.917 r_mcbond_it 0.916 r_symmetry_vdw_other 0.242 r_nbd_other 0.203 r_nbd_refined 0.2 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.156 r_mcbond_other 0.156 r_chiral_restr 0.084 r_nbtor_other 0.084 r_symmetry_vdw_refined 0.064 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2363 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 26
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing