5NI4

Crystal structure of human LTA4H mutant E271A in complex with LTA4 (crystal form II)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NI2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2948% (w/v) PEG 20 000, 15% (w/v) PEG MME 550, 100 mM MES/imidazole pH 6.9, 20 mM of each alcohol (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol)
Crystal Properties
Matthews coefficientSolvent content
2.3948.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 139.56α = 90
b = 139.56β = 90
c = 87.95γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.89549.8199.930.18850.080850.9946.616.415208222.08
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8951.96399.61.6090.69450.3510.936.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5NI21.89549.8071.96152057810799.930.16360.16150.2
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.503
f_angle_d0.844
f_chiral_restr0.048
f_bond_d0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14562
Nucleic Acid Atoms
Solvent Atoms2056
Heterogen Atoms107

Software

Software
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing