3HWW

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2950.5-0.6M tri-Na citrate, 1mM oxoglutarate, 5mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4850.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.91α = 90
b = 117.91β = 90
c = 175.276γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270mirrors2008-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4A1.0000PAL/PLS4A

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
11.955094.20.080.0418.28851858089038.5
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)
11.952.0284.90.180.41.854.47553

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2JLC1.9534.328518580890424494.210.211040.208810.25453RANDOM38.501
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.243
r_dihedral_angle_4_deg19.952
r_dihedral_angle_3_deg18.283
r_dihedral_angle_1_deg7.159
r_scangle_it4.786
r_scbond_it3.084
r_angle_refined_deg1.973
r_mcangle_it1.94
r_mcbond_it1.085
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.243
r_dihedral_angle_4_deg19.952
r_dihedral_angle_3_deg18.283
r_dihedral_angle_1_deg7.159
r_scangle_it4.786
r_scbond_it3.084
r_angle_refined_deg1.973
r_mcangle_it1.94
r_mcbond_it1.085
r_chiral_restr0.149
r_bond_refined_d0.02
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8322
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms97

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling