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Crystal structure of Mmi1 YTH domain complex with RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100 mM MES, 18% (w/v) PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.527 α = 90 b = 77.527 β = 90 c = 65.529 γ = 120
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 QUANTUM 315r 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U
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 1.8 38.76 99.9 0.149 25.4 11.5 20917 20848
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 1.8 1.86 99.6 0.602 11.5
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 4R3I 1.8 38.76 19833 1084 99.92 0.1778 0.1758 0.1844 0.2159 0.2211 RANDOM 14.057
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] 0.21 0.1 0.21 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.838 r_sphericity_free 33.342 r_dihedral_angle_4_deg 14.991 r_dihedral_angle_3_deg 11.506 r_dihedral_angle_1_deg 6.472 r_sphericity_bonded 5.267 r_rigid_bond_restr 2.414 r_angle_other_deg 1.428 r_angle_refined_deg 1.277 r_mcangle_it 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.838 r_sphericity_free 33.342 r_dihedral_angle_4_deg 14.991 r_dihedral_angle_3_deg 11.506 r_dihedral_angle_1_deg 6.472 r_sphericity_bonded 5.267 r_rigid_bond_restr 2.414 r_angle_other_deg 1.428 r_angle_refined_deg 1.277 r_mcangle_it 1.08 r_mcbond_it 0.844 r_mcbond_other 0.815 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1304 Nucleic Acid Atoms 143 Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing