2G3N

Crystal structure of the Sulfolobus solfataricus alpha-glucosidase MalA in complex with beta-octyl-glucopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G3MA trimmed version of the trimer in PDB code 2G3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229810 % PEG 4000, 0.2 M sodium citrate, 0.1 M sodium acetate, 0.5 % beta-octyl-glucopyranoside, microseeding, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4649.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.09α = 90
b = 174.43β = 109.05
c = 144.03γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9340ESRFID14-1

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
12.524.295.20.06511.672.615488534.5
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)
2.52.630.295.32.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTA trimmed version of the trimer in PDB code 2G3M2.5524.16154885145907730096.30.1910.1910.213RANDOM43.2
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]
16.627.9-5.3-11.32
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it3.07
c_mcangle_it2
c_scbond_it1.96
c_angle_deg1.3
c_mcbond_it1.2
c_improper_angle_d0.78
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it3.07
c_mcangle_it2
c_scbond_it1.96
c_angle_deg1.3
c_mcbond_it1.2
c_improper_angle_d0.78
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms34098
Nucleic Acid Atoms
Solvent Atoms615
Heterogen Atoms84

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata reduction