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Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by soman
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 6.6 293 PH 6.6, pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.47 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.084 α = 90 b = 82.697 β = 115.33 c = 96.692 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 ROSENBAUM-ROCK 2006-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C
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 1.7 50 96.4 0.057 19.97 3.7 87071 87071 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) 1.7 1.76 73.1 0.261 2.36 1.9
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 1.7 50 1 87071 82693 4376 96.2 0.18321 0.1817 0.1818 0.21197 RANDOM 24.57
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] -0.72 0.23 0.88 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.356 r_dihedral_angle_4_deg 14.257 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 6.145 r_scangle_it 3.618 r_scbond_it 2.318 r_mcangle_it 1.552 r_angle_refined_deg 1.334 r_mcbond_it 0.915 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.356 r_dihedral_angle_4_deg 14.257 r_dihedral_angle_3_deg 13.946 r_dihedral_angle_1_deg 6.145 r_scangle_it 3.618 r_scbond_it 2.318 r_mcangle_it 1.552 r_angle_refined_deg 1.334 r_mcbond_it 0.915 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.175 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6016 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 53
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing