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Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WQN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M HEPES pH 7.5, 20% PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.05 40.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.108 α = 90 b = 74.293 β = 90 c = 151.139 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 PIXEL DECTRIS PILATUS3 6M 2018-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97892 SSRF BL19U1
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 1.95 30 99.6 0.145 15.25 10.6 57240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4WQN 1.95 30 47044 2513 86.27 0.20223 0.19942 0.2076 0.25577 0.2631 RANDOM 30.742
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] -0.19 0.51 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.569 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_1_deg 7.492 r_long_range_B_refined 7 r_long_range_B_other 7 r_scangle_other 4.763 r_mcangle_other 4.296 r_mcangle_it 4.295 r_scbond_it 3.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.569 r_dihedral_angle_4_deg 15.38 r_dihedral_angle_3_deg 14.592 r_dihedral_angle_1_deg 7.492 r_long_range_B_refined 7 r_long_range_B_other 7 r_scangle_other 4.763 r_mcangle_other 4.296 r_mcangle_it 4.295 r_scbond_it 3.002 r_scbond_other 2.999 r_mcbond_it 2.677 r_mcbond_other 2.665 r_angle_refined_deg 1.885 r_angle_other_deg 1.083 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5080 Nucleic Acid Atoms 374 Solvent Atoms 217 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing