3DT9

Crystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Soman


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WABPDB ENTRY 1WAB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298Ammonium sulfate, Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6954.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.356α = 90
b = 81.356β = 90
c = 72.969γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKUOSMIC BLUE2003-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
11.8570.5396.60.07923.446.5233972339711
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)
1.851.9288.90.4512.513.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1WAB1.853012132421324115792.820.21120.210310.22831RANDOM21.544
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]
-0.23-0.11-0.230.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_4_deg19.434
r_dihedral_angle_3_deg14.351
r_dihedral_angle_1_deg4.103
r_scangle_it3.783
r_scbond_it2.517
r_mcangle_it1.649
r_mcbond_it1.321
r_angle_refined_deg1.268
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_4_deg19.434
r_dihedral_angle_3_deg14.351
r_dihedral_angle_1_deg4.103
r_scangle_it3.783
r_scbond_it2.517
r_mcangle_it1.649
r_mcbond_it1.321
r_angle_refined_deg1.268
r_nbtor_refined0.313
r_nbd_refined0.246
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.132
r_chiral_restr0.095
r_symmetry_hbond_refined0.084
r_bond_refined_d0.013
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms1665
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACphasing