3D5E

Crystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by paraoxon


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D59NATIVE STRUCTURE, PDB ENTRY 3D59

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4749.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.213α = 90
b = 78.696β = 101.61
c = 97.34γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315SI(111) ROSENBAUM-ROCK2006-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15094.90.05319.593.4481621
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.1873.80.1933.432.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNATIVE STRUCTURE, PDB ENTRY 3D592.15014994645723243994.890.2070.2040.261RANDOM29.899
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]
0.12-0.050.38-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.843
r_dihedral_angle_3_deg17.46
r_dihedral_angle_4_deg15.648
r_dihedral_angle_1_deg7.414
r_scangle_it4.917
r_scbond_it3.385
r_mcangle_it2.069
r_angle_refined_deg1.905
r_mcbond_it1.604
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.843
r_dihedral_angle_3_deg17.46
r_dihedral_angle_4_deg15.648
r_dihedral_angle_1_deg7.414
r_scangle_it4.917
r_scbond_it3.385
r_mcangle_it2.069
r_angle_refined_deg1.905
r_mcbond_it1.604
r_nbtor_refined0.309
r_symmetry_vdw_refined0.232
r_nbd_refined0.209
r_xyhbond_nbd_refined0.178
r_chiral_restr0.13
r_symmetry_hbond_refined0.082
r_bond_refined_d0.023
r_gen_planes_refined0.009
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 AtomsNumber
Protein Atoms6013
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms16

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing