3OY7

Crystal structure of a virus encoded glycosyltransferase in complex with GDP-mannose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298crystallization solution:100mM Tris-HCl pH7.0, 20% w/v PEG3350 soaking solution: 100mM Tris-HCl pH7.0, 20% w/v PEG3350, 10mM GDP-mannose , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3963.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.248α = 90
b = 243.189β = 90
c = 67.402γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMarCCD 3002009-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.98APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.75098.40.0910.09119.13425933711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.742.8486.70.5660.5662.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.73130.193425931999170198.690.258540.256870.28965RANDOM31.923
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]
6.07-1.16-4.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.643
r_dihedral_angle_3_deg18.406
r_dihedral_angle_4_deg17.32
r_dihedral_angle_1_deg5.047
r_angle_refined_deg1.06
r_scangle_it0.867
r_scbond_it0.511
r_mcangle_it0.419
r_mcbond_it0.22
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.643
r_dihedral_angle_3_deg18.406
r_dihedral_angle_4_deg17.32
r_dihedral_angle_1_deg5.047
r_angle_refined_deg1.06
r_scangle_it0.867
r_scbond_it0.511
r_mcangle_it0.419
r_mcbond_it0.22
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6202
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms78

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing