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Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Soman
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 6.5 298 Ammonium sulfate, Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.356 α = 90 b = 81.356 β = 90 c = 72.969 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 2003-09-05 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 1.85 70.53 96.6 0.079 23.44 6.5 23397 23397 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) 1.85 1.92 88.9 0.451 2.51 3.8
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 1.85 30 1 21324 21324 1157 92.82 0.2112 0.21031 0.2092 0.22831 RANDOM 21.544
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] -0.23 -0.11 -0.23 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 19.434 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 4.103 r_scangle_it 3.783 r_scbond_it 2.517 r_mcangle_it 1.649 r_mcbond_it 1.321 r_angle_refined_deg 1.268 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 19.434 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 4.103 r_scangle_it 3.783 r_scbond_it 2.517 r_mcangle_it 1.649 r_mcbond_it 1.321 r_angle_refined_deg 1.268 r_nbtor_refined 0.313 r_nbd_refined 0.246 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 1665 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling CNS phasing REFMAC phasing