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Crystal Structure of Factor VIIa in complex with cyclohexanamine
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 67.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.239 α = 90 b = 95.239 β = 90 c = 116.562 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 1.54178
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 1.98 50 99.6 0.125 7.4 30.5 37912
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.05 95.8 17 3555
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 49.69 33713 1775 93.21 0.1737 0.1721 0.1853 0.2041 0.2129 RANDOM 33.369
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] -0.51 -0.51 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.362 r_dihedral_angle_4_deg 18.304 r_dihedral_angle_3_deg 14.786 r_dihedral_angle_1_deg 6.194 r_scangle_it 2.626 r_scbond_it 1.721 r_mcangle_it 1.396 r_angle_refined_deg 1.275 r_mcbond_it 0.914 r_angle_other_deg 0.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.362 r_dihedral_angle_4_deg 18.304 r_dihedral_angle_3_deg 14.786 r_dihedral_angle_1_deg 6.194 r_scangle_it 2.626 r_scbond_it 1.721 r_mcangle_it 1.396 r_angle_refined_deg 1.275 r_mcbond_it 0.914 r_angle_other_deg 0.866 r_symmetry_vdw_other 0.22 r_nbd_other 0.203 r_nbd_refined 0.191 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.161 r_mcbond_other 0.159 r_symmetry_hbond_refined 0.141 r_nbtor_other 0.081 r_chiral_restr 0.078 r_symmetry_vdw_refined 0.061 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2376 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 43
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing