2WGT

Structure of human adenovirus serotype 37 fibre head in complex with a sialic acid derivative, O-Methyl 5-N-propaonyl-3,5-dideoxy-D- glycero-a-D-galacto-2-nonulopyranosylonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UXAPDB ENTRY 1UXA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125-27 % POLYETHYLENE GLYCOL 8000, 50 MM ZINC ACETATE, AND 100 MM HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4349

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.27α = 90
b = 69.99β = 94.42
c = 75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.83099.80.0418.43.7458545
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)
11.81.999.80.472.883.73

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1UXA1.83055584295399.80.1850.1830.226RANDOM19.36
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]
0.640.580.64-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.63
r_dihedral_angle_3_deg12.066
r_dihedral_angle_4_deg9.781
r_dihedral_angle_1_deg6.533
r_scangle_it1.922
r_scbond_it1.337
r_angle_refined_deg1.225
r_mcangle_it1.094
r_angle_other_deg0.864
r_mcbond_it0.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.63
r_dihedral_angle_3_deg12.066
r_dihedral_angle_4_deg9.781
r_dihedral_angle_1_deg6.533
r_scangle_it1.922
r_scbond_it1.337
r_angle_refined_deg1.225
r_mcangle_it1.094
r_angle_other_deg0.864
r_mcbond_it0.655
r_symmetry_vdw_refined0.237
r_nbd_other0.184
r_nbtor_refined0.172
r_nbd_refined0.171
r_metal_ion_refined0.161
r_xyhbond_nbd_refined0.135
r_symmetry_vdw_other0.135
r_mcbond_other0.129
r_symmetry_hbond_refined0.125
r_nbtor_other0.082
r_chiral_restr0.074
r_symmetry_metal_ion_refined0.023
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4361
Nucleic Acid Atoms
Solvent Atoms715
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing