2OBE

Crystal Structure of Chimpanzee Adenovirus (Type 68/Simian 25) Major Coat Protein Hexon


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RUXPDB entry 1RUX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52950.1 M sodium cacodylate, 0.2 M ammonium phosphate, 45% 2-methyl-2,4-pentanediol (MPD), pH 5.0, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4950.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.8α = 90
b = 433β = 90
c = 159.3γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRANDEIS - B42002-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.100NSLSX12C

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
12.19997.70.08915.713.1177830
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)
12.12.1887.80.2534.32.815823

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 1RUX2.149.2717779520251000.1690.1690.21RANDOM37.687
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]
2.49-3.110.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg21.698
r_dihedral_angle_3_deg14.768
r_dihedral_angle_1_deg7.141
r_scangle_it2.267
r_mcangle_it2.135
r_angle_refined_deg1.828
r_scbond_it1.677
r_mcbond_it1.457
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.622
r_dihedral_angle_4_deg21.698
r_dihedral_angle_3_deg14.768
r_dihedral_angle_1_deg7.141
r_scangle_it2.267
r_mcangle_it2.135
r_angle_refined_deg1.828
r_scbond_it1.677
r_mcbond_it1.457
r_nbtor_refined0.322
r_symmetry_vdw_refined0.276
r_symmetry_hbond_refined0.25
r_nbd_refined0.225
r_xyhbond_nbd_refined0.179
r_chiral_restr0.142
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21511
Nucleic Acid Atoms
Solvent Atoms1521
Heterogen Atoms302

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSrefinement