3ZU6

The 3-dimensional structure of MpgP from Thermus thermophilus HB27, in complex with the alpha-mannosylglycerate and orthophosphate reaction products.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZTYPDB ENTRY 3ZTY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5SEE REMARK 1 REFERENCE ABOVE., pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.346.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.93α = 90
b = 70.53β = 95.7
c = 92.63γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDBENT CYLINDRICAL MIRROR2010-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.950950.137.92.9114899-331.04
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)
11.892.0185.70.731.932.6

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 3ZTY1.920.8520.3538647195095.730.18510.18230.2376
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]
4.29320.95520.3953-4.6885
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.532
f_angle_d1.114
f_chiral_restr0.072
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3863
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms24

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing