7KF3

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UZH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5287Microlytic Morpheus screen D12: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each 1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol: 100mM bicine/Trizma base pH 8.5: Braba.00085.a.AE1.PW38674 at 29.4mg/ml: tray 311690 d12: cryo: direct: puck zdr6-4.
Crystal Properties
Matthews coefficientSolvent content
3.259.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.13α = 89.06
b = 93.3β = 78.91
c = 93.77γ = 87.51
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Beryllium Lenses2019-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.3548.3596.10.0470.0640.99812.132.1987864349.532
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4196.10.4180.5620.8082.012.211

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5UZH2.3548.351.9878600197396.10.17510.17430.2101047.4039
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_d14.331
f_angle_d0.747
f_chiral_restr0.046
f_plane_restr0.006
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11350
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms344

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building