3MOY

Crystal structure of probable enoyl-CoA hydratase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289JCSG+ screen condition D7, 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4 with 20% ethylene glycol as cryo-protectant, 41.4 mg/mL protein in Tris buffer with 0.3 M NaCl and 10% glycerol, crystal tracking ID 215265d7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3547.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.88α = 90
b = 84.88β = 90
c = 63.54γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152010-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97946ALS5.0.3

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
11.535.2999.90.03832.79.0741710-324.77
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)
11.51.5499.80.6093.88.94

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 3H811.535.2941665209999.780.1540.1530.168RANDOM20.39
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]
-0.01-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.057
r_dihedral_angle_4_deg16.72
r_dihedral_angle_3_deg12.279
r_dihedral_angle_1_deg5.281
r_scangle_it3.597
r_scbond_it2.171
r_angle_refined_deg1.296
r_mcangle_it1.266
r_mcbond_it0.713
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.057
r_dihedral_angle_4_deg16.72
r_dihedral_angle_3_deg12.279
r_dihedral_angle_1_deg5.281
r_scangle_it3.597
r_scbond_it2.171
r_angle_refined_deg1.296
r_mcangle_it1.266
r_mcbond_it0.713
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1928
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms34

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction