3FTY

Leukotriene A4 hydrolase in complex with fragment 3-(benzyloxy)pyridin-2-amine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FH7PDB entry 3FH7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528913% PEG 8000, 100 mM Imidazole pH 6.5, 100 mM Na Acetate, 5 mM YbCl3, crystal soaked in 13% PEG 8000, 100 mM Imidazole, 100 mM Sodium Acetate, 150 mM NaCl, soak with 5 mM 3-(benzyloxy)pyridin-2-amine, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4349.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.148α = 90
b = 87.079β = 90
c = 99.239γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442008-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
12.155098.10.1855.9336802
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)
2.152.2388.90.5382

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 REPLACEMENTTHROUGHOUTPDB entry 3FH72.15503675818350.2080.2060.257RANDOM17.02
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]
0.28-0.970.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.466
r_dihedral_angle_4_deg16.46
r_dihedral_angle_3_deg14.148
r_dihedral_angle_1_deg5.95
r_scangle_it2.824
r_scbond_it1.744
r_angle_refined_deg1.279
r_mcangle_it0.893
r_mcbond_it0.479
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.466
r_dihedral_angle_4_deg16.46
r_dihedral_angle_3_deg14.148
r_dihedral_angle_1_deg5.95
r_scangle_it2.824
r_scbond_it1.744
r_angle_refined_deg1.279
r_mcangle_it0.893
r_mcbond_it0.479
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms4844
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms39

Software

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