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Crystal Structure of Factor VIIa in complex with cyclohexylmethanamine
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 3.76 67.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.298 α = 90 b = 95.298 β = 90 c = 116.041 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 2007-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5419
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 1.98 50 98.1 0.128 7.3 6.9 37204
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 1.98 2.05 81.5 0.912 3.7 3013
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 1.98 47.67 30785 1622 85.92 0.186 0.1846 0.1946 0.2145 0.2182 RANDOM 30.461
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] -0.53 -0.53 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.058 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_1_deg 6.244 r_scangle_it 2.689 r_scbond_it 1.748 r_mcangle_it 1.453 r_angle_refined_deg 1.296 r_mcbond_it 0.936 r_angle_other_deg 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.058 r_dihedral_angle_4_deg 17.605 r_dihedral_angle_3_deg 14.807 r_dihedral_angle_1_deg 6.244 r_scangle_it 2.689 r_scbond_it 1.748 r_mcangle_it 1.453 r_angle_refined_deg 1.296 r_mcbond_it 0.936 r_angle_other_deg 0.872 r_symmetry_vdw_other 0.204 r_nbd_other 0.202 r_nbd_refined 0.188 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.169 r_mcbond_other 0.157 r_symmetry_hbond_refined 0.143 r_nbtor_other 0.082 r_chiral_restr 0.076 r_metal_ion_refined 0.062 r_symmetry_vdw_refined 0.052 r_bond_refined_d 0.012 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 2376 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 40
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing