3QK8

Crystal structure of enoyl-coA hydratase EchA15 from Mycobacterium marinum in complex with an unknown ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WZ8PDB ENTRY 1WZ8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5290Internal tracking number 218997A9. JCSG screen condition A9: 20% PEG3350, 0.2 M ammonium chloride. MymaA.00829.b.A1 PS00862 at 43.78mg/ml., pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.0339.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.99α = 90
b = 129.53β = 108.57
c = 78.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
11.648.88398.40.04523.924.5256184428181397-321.199
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)
11.61.6488.70.31443.67113629

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUTPDB ENTRY 1WZ81.648.883184428181313912298.390.1380.1380.1370.164RANDOM14.753
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]
-0.010.150.36-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.665
r_dihedral_angle_4_deg16.6
r_dihedral_angle_3_deg11.828
r_dihedral_angle_1_deg5.84
r_scangle_it4.014
r_scbond_it2.508
r_angle_refined_deg1.633
r_mcangle_it1.518
r_angle_other_deg1.136
r_mcbond_it0.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.665
r_dihedral_angle_4_deg16.6
r_dihedral_angle_3_deg11.828
r_dihedral_angle_1_deg5.84
r_scangle_it4.014
r_scbond_it2.508
r_angle_refined_deg1.633
r_mcangle_it1.518
r_angle_other_deg1.136
r_mcbond_it0.906
r_mcbond_other0.29
r_chiral_restr0.104
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11683
Nucleic Acid Atoms
Solvent Atoms1292
Heterogen Atoms109

Software

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