2WQ8 | pdb_00002wq8

Glycan labelling using engineered variants of galactose oxidase obtained by directed evolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GOFPDB ENTRIES 1GOF AND 2EID
experimental modelPDB 2EIDPDB ENTRIES 1GOF AND 2EID

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1510% PEG6K, 0.1 M CACL2, 5% GLYCEROL, 10 MM GLCNAC, 50 M ACETATE PH 5.
Crystal Properties
Matthews coefficientSolvent content
3.1460.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.464α = 90
b = 88.464β = 90
c = 410.846γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.1946.691.90.0725.3415.14304829.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.192.2313.40.362.431.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1GOF AND 2EID2.1976.740873217485.330.185150.182120.170.241750.22RANDOM14.489
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]
0.620.310.62-0.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.442
r_dihedral_angle_4_deg21.29
r_dihedral_angle_3_deg15.033
r_dihedral_angle_1_deg7.402
r_scangle_it4.785
r_scbond_it3.302
r_angle_refined_deg2.113
r_mcangle_it1.787
r_mcbond_it1.065
r_chiral_restr0.148
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4826
Nucleic Acid Atoms
Solvent Atoms382
Heterogen Atoms64

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
REFMACphasing
REFMACrefinement