1PT2

Crystal structure of levansucrase (E342A) complexed with sucrose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OYGPDB ENTRY 1oyg

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1141.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.241α = 90
b = 66.951β = 90
c = 123.956γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAC Science DIP-2030B2003-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.073098.22617126171
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.072.1496.9

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1oyg2.1302391223912127598.370.190980.19090.188760.23191RANDOM19.211
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]
-0.20.29-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.634
r_angle_refined_deg1.119
r_scangle_it1.004
r_angle_other_deg0.75
r_scbond_it0.67
r_mcangle_it0.359
r_symmetry_vdw_refined0.259
r_symmetry_vdw_other0.257
r_nbd_other0.234
r_mcbond_it0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.634
r_angle_refined_deg1.119
r_scangle_it1.004
r_angle_other_deg0.75
r_scbond_it0.67
r_mcangle_it0.359
r_symmetry_vdw_refined0.259
r_symmetry_vdw_other0.257
r_nbd_other0.234
r_mcbond_it0.212
r_nbd_refined0.187
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.136
r_nbtor_other0.081
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3438
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing