3QMJ

Crystal structure of Enoyl-CoA hydratase EchA8_6 from Mycobacterium marinum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FDUPDB ENTRY 3FDU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.7290Internal tracking number 218458A5. JCSG screen condition A5: 20% PEG3350, 0.2 M Magnesium formate. MymaA.00358.c.A1 PS00818 at 69.82 mg/ml., pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4148.906

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.82α = 90
b = 115.82β = 90
c = 115.82γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-02-03MSINGLE 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
12.233.4399.50.07423.627.81329413222-337.348
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)
12.22.2696.70.4615.87.1972

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 DIFFRACTIONMRTHROUGHOUTPDB ENTRY 3FDU2.233.431316665099.230.1850.1830.217RANDOM31.051
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_deg35.505
r_dihedral_angle_4_deg20.292
r_dihedral_angle_3_deg11.396
r_dihedral_angle_1_deg6.058
r_scangle_it3.324
r_scbond_it2.022
r_angle_refined_deg1.328
r_mcangle_it1.295
r_angle_other_deg0.955
r_mcbond_it0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.505
r_dihedral_angle_4_deg20.292
r_dihedral_angle_3_deg11.396
r_dihedral_angle_1_deg6.058
r_scangle_it3.324
r_scbond_it2.022
r_angle_refined_deg1.328
r_mcangle_it1.295
r_angle_other_deg0.955
r_mcbond_it0.69
r_mcbond_other0.14
r_chiral_restr0.078
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1542
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms6

Software

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