8AVA

Leukotriene A4 hydrolase in complex with 4-(4-benzylphenyl)-oxazol-2-amine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L2L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829312% PEG 8000, 100 mM sodium acetate, 5 mM ytterbium chloride, 100 mM imidazole pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.3748.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.072α = 90
b = 87.094β = 90
c = 99.271γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9763MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.35449.63695.980.1240.1290.0350.996912.23713.27105873
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3541.48873.41.731.8140.5370.488911.05

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4L2L1.35449.636100709516472.830.14670.14560.1689RANDOM18.376
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]
-0.570.090.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.931
r_dihedral_angle_4_deg19.885
r_dihedral_angle_3_deg13.121
r_dihedral_angle_1_deg6.574
r_angle_refined_deg1.953
r_angle_other_deg1.577
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.931
r_dihedral_angle_4_deg19.885
r_dihedral_angle_3_deg13.121
r_dihedral_angle_1_deg6.574
r_angle_refined_deg1.953
r_angle_other_deg1.577
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4853
Nucleic Acid Atoms
Solvent Atoms647
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction