3QKA

Crystal structure of enoyl-CoA hydratase EchA5 from Mycobacterium marinum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H81PDB ENTRY 3H81

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5289Crystal tracking ID 218457h19. JCSG+ screen condition H10: 0.2 M ammonium acetate, 0.1 M Bis-Tris propane, 25% PEG3350, 46.3 mg/mL MymaA.00386.a.A1 PS00820, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1241.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.04α = 90
b = 118.92β = 90
c = 132.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+VariMax2011-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT

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
12.155097.40.09211.0847540473428-331.017
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)
12.152.2190.70.4612.442.65531

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 3H812.155073236369897.130.17060.16830.2134RANDOM24.4438
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]
-1.340.710.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.912
r_dihedral_angle_4_deg18.456
r_dihedral_angle_3_deg12.948
r_dihedral_angle_1_deg5.868
r_scangle_it3.299
r_scbond_it2.106
r_angle_refined_deg1.411
r_mcangle_it1.148
r_mcbond_it0.63
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.912
r_dihedral_angle_4_deg18.456
r_dihedral_angle_3_deg12.948
r_dihedral_angle_1_deg5.868
r_scangle_it3.299
r_scbond_it2.106
r_angle_refined_deg1.411
r_mcangle_it1.148
r_mcbond_it0.63
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10339
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction