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Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A2Q pdbid 5A2Q (40S subunit only)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.1 298.15 50 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 Matthews coefficient Solvent content 4.05 69.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 334.67 α = 90 b = 597.13 β = 120.29 c = 336.5 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 6 120 99.4 5.5 6.8 282736
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE pdbid 5A2Q (40S subunit only) 6 116.931 1.34 281673 14432 99.33 0.3227 0.3228 0.3228 0.3207 0.3201 204.98
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 Key Refinement Restraint Deviation f_dihedral_angle_d 16.998 f_angle_d 0.999 f_chiral_restr 0.034 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 249168 Nucleic Acid Atoms 221400 Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing