3NJD

Crystal structure of enoyl-coa hydratase from mycobacterium smegmatis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290MD PACT SCEEN H12: 200MM NAMALONATE, 100M BISTRISPROPANE, 20% PEG 3350; protein at 27MG/ML, CRYO: 15% EDO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.0459

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 171.01α = 90
b = 171.01β = 90
c = 171.01γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.755099.60.05320.14.88331483011-316.1
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)
11.751.898.30.4572.12.35999

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3NJB1.7542.758290382903408799.50.1450.1450.1440.165RANDOM13.01
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_deg38.613
r_dihedral_angle_4_deg12.73
r_dihedral_angle_3_deg11.27
r_dihedral_angle_1_deg5.325
r_scangle_it3.711
r_scbond_it2.402
r_angle_refined_deg1.506
r_mcangle_it1.502
r_angle_other_deg0.996
r_mcbond_it0.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.613
r_dihedral_angle_4_deg12.73
r_dihedral_angle_3_deg11.27
r_dihedral_angle_1_deg5.325
r_scangle_it3.711
r_scbond_it2.402
r_angle_refined_deg1.506
r_mcangle_it1.502
r_angle_other_deg0.996
r_mcbond_it0.875
r_mcbond_other0.288
r_chiral_restr0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4367
Nucleic Acid Atoms
Solvent Atoms641
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling