6MWN

Crystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KZEFab BL3-6 4KZE, 3IVK
experimental modelPDB 3IVKFab BL3-6 4KZE, 3IVK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52950.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.149α = 90
b = 100.582β = 90
c = 236.594γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 16M2017-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033202APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.83829.60799.60.10040.10880.041580.99913.896.84256574.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.8382.9496.40.5240.5951.386.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEFab BL3-6 4KZE, 3IVK2.83829.6071.3842533171899.540.18560.18560.2522
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
f_dihedral_angle_d14.003
f_angle_d1.18
f_chiral_restr0.055
f_bond_d0.009
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6696
Nucleic Acid Atoms3934
Solvent Atoms180
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing