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Crystal Structure of Factor VIIa in complex with N-[[4-(aminomethyl)-2-(2-amino-2-oxoethoxy)phenyl]methyl]-2-(4-hydroxyphenyl)-2-methoxyacetamide;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 3.77 67.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.402 α = 90 b = 95.402 β = 90 c = 116.322 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 2007-03-19 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 1.56 50 96.4 0.062 14.3 2.9 74176
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 1.56 1.62 93.2 0.445 2.7 7059
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 1.56 33.73 65645 3506 89.91 0.1861 0.1852 0.1968 0.2025 0.2106 RANDOM 17.436
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] -0.26 -0.26 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.98 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_1_deg 5.797 r_scangle_it 2.342 r_scbond_it 1.528 r_angle_refined_deg 1.181 r_mcangle_it 1.163 r_angle_other_deg 0.832 r_mcbond_it 0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.98 r_dihedral_angle_4_deg 19.777 r_dihedral_angle_3_deg 14.134 r_dihedral_angle_1_deg 5.797 r_scangle_it 2.342 r_scbond_it 1.528 r_angle_refined_deg 1.181 r_mcangle_it 1.163 r_angle_other_deg 0.832 r_mcbond_it 0.754 r_symmetry_vdw_other 0.253 r_nbd_refined 0.202 r_nbd_other 0.199 r_nbtor_refined 0.171 r_symmetry_hbond_refined 0.15 r_mcbond_other 0.136 r_xyhbond_nbd_refined 0.117 r_metal_ion_refined 0.103 r_symmetry_vdw_refined 0.093 r_nbtor_other 0.079 r_chiral_restr 0.076 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 2371 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 38
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing