6NDR

Crystal structure of dTDP-6-deoxy-D-glucose-3,5-epimerase RmlC from Legionella pneumophila Philadelphia 1 in complex with dTDP-4-KETO-L-RHAMNOSE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IXIPDB entry 2ixi as per MorDa

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5285Microlytic MCSG1 screen, condition E4: 200mM Lithium sulfate, 25% PEG 3350, 100mM Tris base / HCl pH 8.5: LepnA.18372.a.B1.PW38444 at 17.2mg/ml. Cryo: 20% EG: tray: 300303e4g8: puck uhg9-6.
Crystal Properties
Matthews coefficientSolvent content
2.5150.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.38α = 90
b = 46.16β = 112.29
c = 102.03γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+RIGAKU VARIMAX2017-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.647.202970.030.033124.24.0365736326.104
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)
11.61.6488.90.3590.4420.8963.022.835

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 REPLACEMENTTHROUGHOUTPDB entry 2ixi as per MorDa1.647.2021.3557344194997.060.15140.15050.1763024.2081
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_d14.821
f_angle_d1.019
f_chiral_restr0.073
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3008
Nucleic Acid Atoms
Solvent Atoms539
Heterogen Atoms117

Software

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