1UP4 | pdb_00001up4

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.85 Angstrom resolution in the monoclinic form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6200 MM CALCIUM ACETATE, 100MM SODIUM ACETATE PH 4.6, 5% PEG 4000. PROTEIN AT 5 MG/ML
Crystal Properties
Matthews coefficientSolvent content
2.856.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.048α = 90
b = 188.315β = 104.52
c = 125.628γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1202002-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.854099.90.1112.34.31030652
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)
12.852.9599.40.3823.44

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.854097911515399.60.1980.1960.23660.2350.2594RANDOM21.19
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]
-0.052.051.74-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.541
r_scangle_it3.42
r_scbond_it2.147
r_angle_refined_deg1.371
r_mcangle_it0.959
r_mcbond_it0.411
r_symmetry_vdw_refined0.265
r_nbd_refined0.216
r_xyhbond_nbd_refined0.154
r_symmetry_hbond_refined0.131
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26200
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
REFMACrefinement