5BUQ

Unliganded Form of O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Subtilis, Solved at 1.98 Angstroms


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IPL3IPL(N-domain of S. aureus MenE), chainA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.152938.1% (w/v) PEG8000, 0.09M cacodylate/HCl pH 6.15, 0.144M calcium acetate, 12.6% glycerol with additive agent of 0.049M sodium phosphate monobasic and 0.091M Potassium phosphate dibasic
Crystal Properties
Matthews coefficientSolvent content
2.4549.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.78α = 90
b = 76.91β = 114.93
c = 93.87γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.973SSRFBL17U

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
11.9833.2798.830.047590.067322.061.973620
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)
11.982.05199.150.20439.051.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3IPL(N-domain of S. aureus MenE), chainA1.9833.271.3473463369998.620.16240.16050.1997
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
f_dihedral_angle_d12.378
f_angle_d0.999
f_chiral_restr0.04
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7039
Nucleic Acid Atoms
Solvent Atoms1035
Heterogen Atoms5

Software

Software
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHENIXphasing
Cootmodel building