3QRE

Crystal structure of an enoyl-coA hydratase EchA12_1 from Mycobacterium marinum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GOWPDB ENTRY 3GOW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528939.66 mg/mL MymaA.00305.a.A1 PS00827 against PACT screen condition F10: 0.02 M Na/K phosphate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 218672f10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.76586630.345789

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.7α = 90
b = 87.7β = 90
c = 87.7γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-01-31MSINGLE 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
12.45099.90.06324.747.190529040-346.082
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)
12.42.461000.5194.337.1667

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 3GOW2.450900247199.450.18210.17960.229RANDOM36.3734
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_deg32.43
r_dihedral_angle_4_deg15.943
r_dihedral_angle_3_deg13.999
r_dihedral_angle_1_deg5.679
r_scangle_it3.251
r_scbond_it1.996
r_angle_refined_deg1.323
r_mcangle_it1.157
r_mcbond_it0.622
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.43
r_dihedral_angle_4_deg15.943
r_dihedral_angle_3_deg13.999
r_dihedral_angle_1_deg5.679
r_scangle_it3.251
r_scbond_it1.996
r_angle_refined_deg1.323
r_mcangle_it1.157
r_mcbond_it0.622
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1443
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms2

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction