7LNU

Ternary complex of the Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus bound to isopentenyl monophosphate and ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LNVcma apo model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2750.1 M Bis-Tris, pH 5.5 28% PEG 3350 0.1 M Sodium Chloride
Crystal Properties
Matthews coefficientSolvent content
2.1442.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.892α = 90
b = 74.503β = 90
c = 171.691γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200KOsmic Veri Max Mirrors2016-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim 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
12.550910.10.0470.99111.94.21871430.42
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.540.6810.3940.651.93

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEcma apo model2.545.391.331835793797.10.23240.22940.286832.43
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_d23.2858
f_angle_d0.6516
f_chiral_restr0.0454
f_plane_restr0.0028
f_bond_d0.0021
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3808
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms119

Software

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