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Crystal Structure of Factor VIIa in complex with phenylmethanamine;hydrochloride
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 67.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.238 α = 90 b = 95.238 β = 90 c = 116.216 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 2007-03-24 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 1.55 50 92.7 0.072 18.3 6.6 71819
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 1.55 1.61 50.8 0.427 2.2 3869
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 1.55 40 65007 3461 88.27 0.1842 0.1836 0.1927 0.1959 0.2034 RANDOM 18.289
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 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.318 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 14.433 r_dihedral_angle_1_deg 5.802 r_scangle_it 2.313 r_scbond_it 1.501 r_mcangle_it 1.166 r_angle_refined_deg 1.147 r_angle_other_deg 0.825 r_mcbond_it 0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.318 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 14.433 r_dihedral_angle_1_deg 5.802 r_scangle_it 2.313 r_scbond_it 1.501 r_mcangle_it 1.166 r_angle_refined_deg 1.147 r_angle_other_deg 0.825 r_mcbond_it 0.738 r_nbd_refined 0.2 r_symmetry_vdw_other 0.2 r_nbd_other 0.199 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.154 r_mcbond_other 0.122 r_xyhbond_nbd_refined 0.116 r_symmetry_vdw_refined 0.093 r_nbtor_other 0.079 r_chiral_restr 0.073 r_metal_ion_refined 0.026 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 343 Heterogen Atoms 39
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing