1UP7 | pdb_00001up7

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with NAD and glucose-6-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSE-MET STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6200 MM CALCIUM ACETATE, 100MM SODIUM ACETATE PH 4.6, 25% PEG500DME, 0.2MM NAD+, 1MM PNP-BETA-D-GLUCOSE-6-PHOSPHATE, 2MM MNS04. PROTEIN AT 5 MG/ML WITH THE COFACTORS IN THE SAME CONCENTRATION AS ABOVE.
Crystal Properties
Matthews coefficientSolvent content
2.856.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.132α = 90
b = 178.132β = 90
c = 278.927γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2003-06-15MSINGLE 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
12.42098.30.08322.46.81708572
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)
12.42.4998.30.4613.55.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSE-MET STRUCTURE2.419.96162307854998.30.2010.1990.20.240.23RANDOM21.05
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]
-0.83-0.831.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.868
r_scangle_it3.135
r_scbond_it1.89
r_angle_refined_deg1.425
r_mcangle_it0.957
r_mcbond_it0.439
r_symmetry_vdw_refined0.217
r_nbd_refined0.208
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.153
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26560
Nucleic Acid Atoms
Solvent Atoms759
Heterogen Atoms490

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling