4B9E

Structure of a putative epoxide hydrolase from Pseudomonas aeruginosa, with bound MFA.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y37PDB ENTRY 1Y37

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M LI2SO4, 1.25 M (NH4)2SO4, 0.1 M TRIS HCL PH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.6766.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.92α = 90
b = 83.92β = 90
c = 140.95γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.436.8399.70.0911.56.299408213.7
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)
11.41.4899.30.692.45

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 1Y371.436.2794130495299.680.111650.11040.13525RANDOM17.522
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.614
r_dihedral_angle_2_deg30.306
r_dihedral_angle_4_deg19.155
r_sphericity_bonded12.522
r_dihedral_angle_3_deg12.136
r_mcbond_other11.304
r_mcbond_it10.937
r_dihedral_angle_1_deg5.334
r_rigid_bond_restr3.69
r_angle_refined_deg1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.614
r_dihedral_angle_2_deg30.306
r_dihedral_angle_4_deg19.155
r_sphericity_bonded12.522
r_dihedral_angle_3_deg12.136
r_mcbond_other11.304
r_mcbond_it10.937
r_dihedral_angle_1_deg5.334
r_rigid_bond_restr3.69
r_angle_refined_deg1.72
r_angle_other_deg0.912
r_symmetry_vdw_refined0.311
r_nbd_refined0.279
r_nbd_other0.221
r_nbtor_refined0.189
r_xyhbond_nbd_refined0.188
r_symmetry_vdw_other0.179
r_symmetry_hbond_refined0.144
r_chiral_restr0.113
r_nbtor_other0.107
r_xyhbond_nbd_other0.091
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2346
Nucleic Acid Atoms
Solvent Atoms417
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing