3HE2

Crystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QQ3pdb entry 2qq3, modified with ccp4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP290HAMPTON INDEX, H11: 30% PEG 2000 MME, 100MM KSCN, MYTUD.01381.A AT 32.5G/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1241.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.12α = 90
b = 76.47β = 90
c = 134.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-2SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.367.1499.60.07867.1418.864.853289032742-334.83
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)
12.32.361000.4874.34.962401

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 DIFFRACTIONMR, MRTHROUGHOUTpdb entry 2qq3, modified with ccp4 program chainsaw2.3503269532695166199.60.190.190.1870.241RANDOM20.95
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]
2.49-2.560.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.528
r_dihedral_angle_4_deg20.729
r_dihedral_angle_3_deg14.031
r_dihedral_angle_1_deg5.876
r_scangle_it3.709
r_scbond_it2.262
r_angle_refined_deg1.477
r_mcangle_it1.329
r_angle_other_deg0.93
r_mcbond_it0.727
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.528
r_dihedral_angle_4_deg20.729
r_dihedral_angle_3_deg14.031
r_dihedral_angle_1_deg5.876
r_scangle_it3.709
r_scbond_it2.262
r_angle_refined_deg1.477
r_mcangle_it1.329
r_angle_other_deg0.93
r_mcbond_it0.727
r_mcbond_other0.167
r_chiral_restr0.083
r_bond_refined_d0.016
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 Atoms5307
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms30

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling