4RVB

Crystal Structure Analysis of the Human Leukotriene A4 Hydrolase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FTX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.229313% PEG 8000, 100MM IMIDAZOLE PH 6.2, 100MM NAACETATE, 5MM YBCL3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.939α = 90
b = 87.153β = 90
c = 99.228γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97852SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9336.2799.87487614869822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9331.98399.6

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 REPLACEMENTTHROUGHOUT3FTX1.9336.2725123248698253499.870.145850.144150.17835RANDOM14.344
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
r_dihedral_angle_2_deg35.833
r_dihedral_angle_4_deg19.339
r_dihedral_angle_3_deg12.772
r_dihedral_angle_1_deg6.678
r_long_range_B_refined6.021
r_long_range_B_other6.021
r_scangle_other3.771
r_scbond_it2.43
r_scbond_other2.43
r_angle_refined_deg1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.833
r_dihedral_angle_4_deg19.339
r_dihedral_angle_3_deg12.772
r_dihedral_angle_1_deg6.678
r_long_range_B_refined6.021
r_long_range_B_other6.021
r_scangle_other3.771
r_scbond_it2.43
r_scbond_other2.43
r_angle_refined_deg1.82
r_mcangle_other1.7
r_mcangle_it1.698
r_mcbond_it1.199
r_mcbond_other1.182
r_angle_other_deg0.893
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4853
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms45

Software

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