3F9C

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


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 DROP6.6293PH 6.6. NATIVE PROTEIN CRYSTAL SOAKED IN MOTHER LIQUOR CONTAINING DFP, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.4748.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.375α = 90
b = 82.4β = 115.64
c = 96.511γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUOSMIC BLUE2008-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
12.3501000.06920.714.2366753667511
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)
2.32.381000.443.234.1

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 3D592.35013667534789182699.940.199190.195950.26109RANDOM36.908
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]
-1.480.460.561.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.302
r_dihedral_angle_4_deg20.355
r_dihedral_angle_3_deg17.355
r_dihedral_angle_1_deg7.823
r_scangle_it3.825
r_scbond_it2.59
r_angle_refined_deg1.813
r_mcangle_it1.752
r_mcbond_it1.058
r_symmetry_vdw_refined0.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.302
r_dihedral_angle_4_deg20.355
r_dihedral_angle_3_deg17.355
r_dihedral_angle_1_deg7.823
r_scangle_it3.825
r_scbond_it2.59
r_angle_refined_deg1.813
r_mcangle_it1.752
r_mcbond_it1.058
r_symmetry_vdw_refined0.352
r_nbtor_refined0.309
r_symmetry_hbond_refined0.291
r_nbd_refined0.231
r_xyhbond_nbd_refined0.167
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5978
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms20

Software

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