3GBD

Crystal structure of the isomaltulose synthase SmuA from Protaminobacter rubrum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M53PDB ENTRY 1M53

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72900.2M tri-Li-citrate, 20% PEG3350, pH7, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.5952.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.63α = 90
b = 81.39β = 90
c = 135.57γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2004-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9803ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9519.90.07213.23.95196312.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.952.050.3154.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M531.9519.89484394879960.1790.1790.224RANDOM21
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]
-0.133.78-3.66
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it3.11
c_scbond_it2.33
c_mcangle_it1.88
c_angle_deg1.6
c_mcbond_it1.39
c_improper_angle_d1.02
c_bond_d0.013
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.8
c_scangle_it3.11
c_scbond_it2.33
c_mcangle_it1.88
c_angle_deg1.6
c_mcbond_it1.39
c_improper_angle_d1.02
c_bond_d0.013
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 Atoms4702
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms45

Software

Software
Software NamePurpose
DNAdata collection
AMoREphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling