X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.12 M Monosaccharides (20 mM D-Glucose; 20 mM D-Mannose; 20 mM D-Galactose; 20 mM L-Fucose; 20 mM D-Xylose; 20 mM N-Acetyl-D-Glucosamine), 0.1 M buffer system 1 pH 6.5 (sodium HEPES and MOPS), and 50 % Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)
Crystal Properties
Matthews coefficientSolvent content
2.7455.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.08α = 90
b = 106.08β = 90
c = 304γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2020-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9792SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1232.0699.90.1330.1360.0270.99916.526.299275
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.122.181002.142.180.4120.67727.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.1232.0694118503399.920.18790.18660.2102RANDOM53.183
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]
-0.03-0.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.068
r_dihedral_angle_4_deg17.09
r_dihedral_angle_3_deg15.266
r_dihedral_angle_1_deg6.269
r_angle_refined_deg1.432
r_angle_other_deg1.329
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.068
r_dihedral_angle_4_deg17.09
r_dihedral_angle_3_deg15.266
r_dihedral_angle_1_deg6.269
r_angle_refined_deg1.432
r_angle_other_deg1.329
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10706
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms112

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing