3OC7

Crystal structure of an enoyl-CoA hydratase from Mycobacterium avium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MYBPDB entry 3myb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528925.9 mg/mL MyavA.01530.a.A1 PW29874 3C cleaved against JCSG+ condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol, crystal tracking ID 216676e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.23α = 90
b = 83.23β = 90
c = 93.82γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-07-31MSINGLE 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
11.5501000.06615.95.43883938836-320.905
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)
11.51.541000.4982.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 3myb1.541.623883938834202099.90.17220.17170.1808RANDOM17.6087
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]
1.021.02-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.728
r_dihedral_angle_4_deg14.377
r_dihedral_angle_3_deg11.051
r_dihedral_angle_1_deg5.082
r_scangle_it3.268
r_scbond_it2.085
r_angle_refined_deg1.317
r_mcangle_it1.144
r_mcbond_it0.629
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.728
r_dihedral_angle_4_deg14.377
r_dihedral_angle_3_deg11.051
r_dihedral_angle_1_deg5.082
r_scangle_it3.268
r_scbond_it2.085
r_angle_refined_deg1.317
r_mcangle_it1.144
r_mcbond_it0.629
r_chiral_restr0.089
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1833
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms4

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction