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YTH domain-containing protein mmi1 and RNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 25% PEG3350, 8% Tacsimate
Crystal Properties Matthews coefficient Solvent content 1.84 33.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.105 α = 90 b = 55.871 β = 90 c = 104.541 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 RIGAKU 2014-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
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 1.54 52.27 93.99 17.4 3.7 43899
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 5EIP 1.54 30 41691 2201 93.95 0.17447 0.17175 0.1753 0.22461 0.2266 RANDOM 27.292
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] 0.46 -1.47 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.763 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_3_deg 11.388 r_long_range_B_refined 7.42 r_long_range_B_other 7.336 r_dihedral_angle_1_deg 6.889 r_scangle_other 4.964 r_mcangle_it 3.681 r_mcangle_other 3.68 r_scbond_it 3.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.763 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_3_deg 11.388 r_long_range_B_refined 7.42 r_long_range_B_other 7.336 r_dihedral_angle_1_deg 6.889 r_scangle_other 4.964 r_mcangle_it 3.681 r_mcangle_other 3.68 r_scbond_it 3.394 r_scbond_other 3.393 r_mcbond_it 2.516 r_mcbond_other 2.506 r_angle_refined_deg 1.848 r_angle_other_deg 1.323 r_chiral_restr 0.127 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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 2528 Nucleic Acid Atoms 334 Solvent Atoms 365 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot data reduction HKL-2000 data scaling PHASER phasing