3EXV

Crystal structure of the human Adenovirus type 11 fiber knob


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H7ZHuman Adenovirus type 3 fiber knob

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293.1518% w/v PEG6000, 0.1M HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
1.7931.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.597α = 90
b = 100.597β = 90
c = 100.597γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDMARMOSAIC 225 mm CCD2006-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.457199.90.04563007928526-314.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.51000.3885.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHuman Adenovirus type 3 fiber knob1.4523.713007928526152599.930.193650.192040.2246RANDOM9.959
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.106
r_dihedral_angle_4_deg12.861
r_dihedral_angle_3_deg10.705
r_dihedral_angle_1_deg8.391
r_scangle_it1.096
r_angle_refined_deg0.918
r_scbond_it0.765
r_angle_other_deg0.679
r_mcangle_it0.615
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.106
r_dihedral_angle_4_deg12.861
r_dihedral_angle_3_deg10.705
r_dihedral_angle_1_deg8.391
r_scangle_it1.096
r_angle_refined_deg0.918
r_scbond_it0.765
r_angle_other_deg0.679
r_mcangle_it0.615
r_mcbond_it0.55
r_symmetry_vdw_other0.21
r_nbd_other0.192
r_nbd_refined0.184
r_nbtor_refined0.174
r_symmetry_vdw_refined0.108
r_xyhbond_nbd_refined0.088
r_nbtor_other0.08
r_symmetry_hbond_refined0.073
r_chiral_restr0.059
r_mcbond_other0.054
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1579
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling