4FDN

Mycobacterium tuberculosis DprE1 in complex with CT325 - hexagonal crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherDPRE1 - MONOCLINIC CRYSTAL FORM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
162880.1 M sodium cacodylate 44% ethylene glycol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.8957.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.7α = 90
b = 127.7β = 90
c = 64.4γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944VARIMAX2012-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.445.3699.90.0930.09320.810.623678
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)
12.42.5399.30.5650.5653.37

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTDPRE1 - MONOCLINIC CRYSTAL FORM2.428.751.4223792359312181000.1840.1820.226
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]
-2.2166-2.21664.4332
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.682
f_angle_d1.158
f_chiral_restr0.074
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3141
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms76

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling