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Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Paraoxon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAB PDB ENTRY 1WAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.27 α = 90 b = 81.27 β = 90 c = 72.506 γ = 120
Symmetry Space Group P 31 2 1
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 RIGAKU OSMIC BLUE 2003-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.1 70.36 92.1 0.058 28.28 5.7 15253 15253 1 1
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) 2.1 2.18 90.6 0.354 3.3 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WAB 2.1 30 1 13973 13973 754 89.03 0.19957 0.19926 0.1947 0.20559 RANDOM 30.629
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] -0.88 -0.44 -0.88 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.4 r_dihedral_angle_4_deg 20.2 r_dihedral_angle_3_deg 12.264 r_scangle_it 3.816 r_dihedral_angle_1_deg 3.784 r_scbond_it 2.574 r_mcangle_it 1.753 r_mcbond_it 1.367 r_angle_refined_deg 1.363 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.4 r_dihedral_angle_4_deg 20.2 r_dihedral_angle_3_deg 12.264 r_scangle_it 3.816 r_dihedral_angle_1_deg 3.784 r_scbond_it 2.574 r_mcangle_it 1.753 r_mcbond_it 1.367 r_angle_refined_deg 1.363 r_nbtor_refined 0.309 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.099 r_symmetry_hbond_refined 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1609 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling CNS phasing REFMAC phasing