5NGY

Crystal structure of Leuconostoc citreum NRRL B-1299 dextransucrase DSR-M


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.528520% PEG3350, 0.2M KSCN, 0.1 Pr(III)acetate, BIS-TRIS pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.7855.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.869α = 90
b = 128.81β = 90
c = 234.518γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2Mmirrors2016-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8729ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
13.75098.30.1950.10.983.64.33438844.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.73.997.30.5280.2840.8221.44

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 REPLACEMENTTHROUGHOUT5lfc3.75032648169398.060.194530.192340.23643RANDOM62.15
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]
-5.870.145.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.562
r_dihedral_angle_4_deg14.208
r_dihedral_angle_3_deg13.266
r_dihedral_angle_1_deg5.845
r_long_range_B_refined3.476
r_long_range_B_other3.476
r_mcangle_it2.267
r_mcangle_other2.267
r_scangle_other2.242
r_mcbond_it1.346
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.562
r_dihedral_angle_4_deg14.208
r_dihedral_angle_3_deg13.266
r_dihedral_angle_1_deg5.845
r_long_range_B_refined3.476
r_long_range_B_other3.476
r_mcangle_it2.267
r_mcangle_other2.267
r_scangle_other2.242
r_mcbond_it1.346
r_mcbond_other1.346
r_scbond_it1.288
r_scbond_other1.288
r_angle_refined_deg1.098
r_angle_other_deg0.83
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18805
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
SCALAdata scaling