4AJB

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with Isocitrate, magnesium(II) and thioNADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AI2PDB ENTRY 1AI2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
11.85M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT
Crystal Properties
Matthews coefficientSolvent content
4.572

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.054α = 90
b = 103.054β = 90
c = 150.339γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DASLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.948.899.40.0818.27.364372-3
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)
11.92.0196.10.543.27.2

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 1AI21.948.7441.9964286323599.890.16710.16630.1805
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]
-1.1201-1.1201-9.8262
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.002
f_angle_d1.079
f_chiral_restr0.073
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3204
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms67

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing