4H19

Crystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TJ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1sitting drop vapor diffuction4298Protein (10 mM Tris, pH 8.0, 200 mM NaCl, 5 mM Mg, 10 mM D-ribonohydroxamate; Reservoir (20% (w/v) PEG-8000, 100 mM Tris pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir, + 20% glycerol, 50 mM MgCl, 10 mM D-ribonohydroxamate), sitting drop vapor diffuction, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.363α = 90
b = 395.688β = 90
c = 177.802γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HEMIRRORS2011-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.8197.8441000.133106.7573535573535
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.999.90.6490.6491.25.883299

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 REPLACEMENTTHROUGHOUT3TJ41.8197.845731755731752877799.90.1390.1390.13710.1755RANDOM17.366
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]
0.810.21-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.305
r_dihedral_angle_4_deg18.887
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg6.481
r_angle_refined_deg1.851
r_angle_other_deg0.931
r_chiral_restr0.123
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.305
r_dihedral_angle_4_deg18.887
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg6.481
r_angle_refined_deg1.851
r_angle_other_deg0.931
r_chiral_restr0.123
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms46512
Nucleic Acid Atoms
Solvent Atoms5793
Heterogen Atoms531

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing