4UMI

Crystal structure of the fiber head domain of the Atadenovirus snake adenovirus 1, native, F23 crystal form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.510 MM TRIS-HCL, 1.7 M AMMONIUM SULFATE, 0.085 M HEPES SODIUM SALT PH 7.5, 1.7%(V/V) POLYETHYLENE GLYCOL (PEG) 400, 15%(V/V) GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
1.727

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.52α = 90
b = 121.52β = 90
c = 121.52γ = 90
Symmetry
Space GroupF 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING2013-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.334399.50.0518.55.83398515.6
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)
11.331.3695.30.372.22.4

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 4D0V CHAIN A1.3342.9632152183299.530.118480.117330.13804RANDOM21.225
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]
-1.742.47-5.69-2.73-2.364.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg25.548
r_dihedral_angle_2_deg25.168
r_dihedral_angle_3_deg12.22
r_sphericity_bonded11.235
r_dihedral_angle_1_deg6.485
r_rigid_bond_restr5.279
r_scangle_it3.865
r_scbond_it3.427
r_mcangle_it2.356
r_mcbond_other1.887
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg25.548
r_dihedral_angle_2_deg25.168
r_dihedral_angle_3_deg12.22
r_sphericity_bonded11.235
r_dihedral_angle_1_deg6.485
r_rigid_bond_restr5.279
r_scangle_it3.865
r_scbond_it3.427
r_mcangle_it2.356
r_mcbond_other1.887
r_mcbond_it1.864
r_angle_refined_deg1.614
r_angle_other_deg0.813
r_symmetry_hbond_refined0.357
r_symmetry_vdw_refined0.347
r_nbd_refined0.252
r_symmetry_hbond_other0.209
r_nbd_other0.192
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.18
r_symmetry_vdw_other0.163
r_chiral_restr0.116
r_nbtor_other0.088
r_xyhbond_nbd_other0.037
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
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_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms859
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing