X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherpreviously solved C. perfringens O-GlcNAcase structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.62932.4M Ammonium Sulfate, 0.1M Hepes
Crystal Properties
Matthews coefficientSolvent content
3.4264.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.489α = 90
b = 178.104β = 90
c = 407.054γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.3203.5394.20.1130.1260.99512.125.122532533.101
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.5595.80.4410.4930.8663.84.8

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 REPLACEMENTTHROUGHOUTpreviously solved C. perfringens O-GlcNAcase structure2.3203.53224244108194.240.20670.20650.2471RANDOM35.238
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]
3.45-0.97-2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.835
r_dihedral_angle_4_deg15.779
r_dihedral_angle_3_deg13.33
r_dihedral_angle_1_deg6.08
r_angle_refined_deg1.41
r_angle_other_deg1.204
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.835
r_dihedral_angle_4_deg15.779
r_dihedral_angle_3_deg13.33
r_dihedral_angle_1_deg6.08
r_angle_refined_deg1.41
r_angle_other_deg1.204
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms27443
Nucleic Acid Atoms
Solvent Atoms1565
Heterogen Atoms483

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction