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Crystal structure of YTH domain of Zygosaccharomyces rouxii MRB1 protein in complex with N6-Methyladenosine RNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 277 0.8 M ammonium dihydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.39 α = 90 b = 117.39 β = 90 c = 380.928 γ = 120
Symmetry Space Group P 61 2 2
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 2014-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9790 NSLS X25
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 2.7 25 94.2 0.137 6.6 4.5 41339 42.55
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 2.7 2.8 96.1 0.498 4.6 4123
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.7 24.921 1.35 37767 1758 94.15 0.2009 0.1988 0.2034 0.2452 0.2477 34.672
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 14.943 f_angle_d 1.336 f_chiral_restr 0.072 f_bond_d 0.015 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7561 Nucleic Acid Atoms 900 Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data reduction SHARP phasing HKL-2000 data scaling PDB_EXTRACT data extraction Coot model building PHENIX refinement CBASS data collection DENZO data reduction SCALEPACK data scaling