3OME

Crystal structure of a probable ENOYL-COA Hydratase from Mycobacterium Smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H8LPDB entry 3h8l

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290EBS JCSG+ SCEEN E11: 160MM CAOAC2, 80MM CACODYLATE PH 6.5, 14.4% PEG 8000, 20% GLYCEROL, MYSMA.00358.E.A1 PS00544 AT 30MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.5351

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.22α = 90
b = 86.65β = 97.93
c = 140.05γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.000ALS5.0.2

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
12.055099.90.07911.894.5108008107914-335.58
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)
12.052.199.80.4972.74.47953

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 3h8l2.0550108008107778537399.80.1470.1470.1450.174RANDOM35.03
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]
0.11-0.471.23-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.108
r_dihedral_angle_4_deg16.15
r_dihedral_angle_3_deg12.559
r_dihedral_angle_1_deg5.432
r_scangle_it3.738
r_scbond_it2.296
r_mcangle_it1.345
r_angle_refined_deg1.34
r_angle_other_deg0.93
r_mcbond_it0.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.108
r_dihedral_angle_4_deg16.15
r_dihedral_angle_3_deg12.559
r_dihedral_angle_1_deg5.432
r_scangle_it3.738
r_scbond_it2.296
r_mcangle_it1.345
r_angle_refined_deg1.34
r_angle_other_deg0.93
r_mcbond_it0.726
r_mcbond_other0.196
r_chiral_restr0.087
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms11189
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms6

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling