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Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by paraoxon
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D59 NATIVE STRUCTURE, PDB ENTRY 3D59
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.213 α = 90 b = 78.696 β = 101.61 c = 97.34 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 315 SI(111) ROSENBAUM-ROCK 2006-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 50 94.9 0.053 19.59 3.4 48162 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 73.8 0.193 3.43 2.1
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 NATIVE STRUCTURE, PDB ENTRY 3D59 2.1 50 1 49946 45723 2439 94.89 0.207 0.204 0.2033 0.261 RANDOM 29.899
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] 0.12 -0.05 0.38 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.843 r_dihedral_angle_3_deg 17.46 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_1_deg 7.414 r_scangle_it 4.917 r_scbond_it 3.385 r_mcangle_it 2.069 r_angle_refined_deg 1.905 r_mcbond_it 1.604 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.843 r_dihedral_angle_3_deg 17.46 r_dihedral_angle_4_deg 15.648 r_dihedral_angle_1_deg 7.414 r_scangle_it 4.917 r_scbond_it 3.385 r_mcangle_it 2.069 r_angle_refined_deg 1.905 r_mcbond_it 1.604 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.13 r_symmetry_hbond_refined 0.082 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 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 6013 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 16
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing