3MYB

Crystal structure of enoyl-coa hydratase mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VX2pdb entry 2vx2 modified with CCP4 program chainsaw

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290EBS JCSG+ SCREEN D1: 24% PEG 1500, 20% GLYCEROL; MYSMA.00358.J AT MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.45α = 90
b = 78.45β = 90
c = 113.43γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
11.55501000.09712.726.7113405113396-322.18
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)
11.551.591000.5133.66.88380

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 2vx2 modified with CCP4 program chainsaw1.5543.54113405113349576599.90.1150.1150.1140.133RANDOM12.01
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]
2.042.04-4.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.404
r_dihedral_angle_4_deg16.196
r_dihedral_angle_3_deg12.307
r_dihedral_angle_1_deg4.922
r_scangle_it3.604
r_scbond_it2.227
r_angle_refined_deg1.508
r_mcangle_it1.365
r_angle_other_deg0.99
r_mcbond_it0.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.404
r_dihedral_angle_4_deg16.196
r_dihedral_angle_3_deg12.307
r_dihedral_angle_1_deg4.922
r_scangle_it3.604
r_scbond_it2.227
r_angle_refined_deg1.508
r_mcangle_it1.365
r_angle_other_deg0.99
r_mcbond_it0.835
r_mcbond_other0.275
r_chiral_restr0.091
r_bond_refined_d0.015
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 Atoms5727
Nucleic Acid Atoms
Solvent Atoms938
Heterogen Atoms24

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling