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Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 30% PENTAERYTHRITOL ETHOXYLATE (15/4EO/OH) (V/V), 50 MM AMMONIUM SULPHATE,50 MM BIS-TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.56 α = 90 b = 72.98 β = 90 c = 73.21 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.95 20 90.9 0.12 10.2 4.9 7000
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3 96.5 0.42 2.9 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.95 51.71 6685 315 91.2 0.223 0.221 0.2121 0.259 0.2503 RANDOM 7.58
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] 0.08 0.17 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.625 r_dihedral_angle_4_deg 26.704 r_dihedral_angle_3_deg 17.015 r_dihedral_angle_1_deg 5.358 r_angle_refined_deg 1.229 r_scangle_it 1.156 r_scbond_it 0.665 r_mcangle_it 0.516 r_nbtor_refined 0.299 r_mcbond_it 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.625 r_dihedral_angle_4_deg 26.704 r_dihedral_angle_3_deg 17.015 r_dihedral_angle_1_deg 5.358 r_angle_refined_deg 1.229 r_scangle_it 1.156 r_scbond_it 0.665 r_mcangle_it 0.516 r_nbtor_refined 0.299 r_mcbond_it 0.29 r_symmetry_hbond_refined 0.271 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2452 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling SHELXD phasing SHARP phasing DM phasing