5VYC

Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.1298.1550 mM HEPES-NaOH, 50 mM NH4 acetate, 50 mM NH4Cl, 1 mM Mg acetate, 2 mM CaCl2, 3% PEG 20000, 3% PEG 3350, 2 mM TCEP, pH 8.1
Crystal Properties
Matthew coefficientSolvent content
4.0569.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 334.67α = 90
b = 597.13β = 120.29
c = 336.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1612099.45.56.8282736

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-VALUEpdbid 5A2Q (40S subunit only)6116.9311.342816731443299.330.32270.32280.3207204.98
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_d16.998
f_angle_d0.999
f_chiral_restr0.034
f_bond_d0.01
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms249168
Nucleic Acid Atoms221400
Solvent Atoms
Heterogen Atoms6

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing