3POC

The crystal structure of the D307A mutant of alpha-Glucosidase (FAMILY 31) from Ruminococcus obeum ATCC 29174 in complex with acarbose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N04PDB ENTRY 3N04

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52890.1M BIS-TRIS, 25% PEG3350, 10% ACARBOSE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.954α = 90
b = 125.691β = 107.62
c = 87.968γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRROR2010-04-22MSINGLE 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 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
11.9942960.10312.23.49180391803
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)
22.0384.90.5851.162.7

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3N041.9941.3658066880967409784.070.17050.16760.2246
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]
22.36084.9589-8.6732-13.6876
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.835
f_angle_d1.028
f_chiral_restr0.074
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10866
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms86

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling