4IMA

The structure of C436M-hLPYK in complex with Citrate/Mn/ATP/Fru-1,6-BP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VGBPDB ENTRY 2VGB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.92775% PEG6000, 0.05 M potassium citrate, 2.64 uM manganese chloride, pH 4.9, EVAPORATION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1160.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.751α = 90
b = 204.727β = 96.75
c = 86.532γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97921APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.955097.70.07414.93.7200629
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0286.10.5181.42.9

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 2VGB1.95438.8910.09179645901187.270.20.19830.2332
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]
3.4947-20.7131-8.42524.9305
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.382
f_angle_d1.047
f_chiral_restr0.069
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15095
Nucleic Acid Atoms
Solvent Atoms859
Heterogen Atoms159

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing