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The structure of the tRNA-specific deaminase from M. capricolum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 277 0.49M sodium phosphate monobasic monohydrate, 0.91M potassium phosphate dibasic, pH 6.9
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.138 α = 90 b = 49.138 β = 90 c = 147.931 γ = 90
Symmetry Space Group P 43 21 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 CCD OXFORD ONYX CCD 2019-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.4 21.07 99.8 0.1 0.998 15.6 6.6 7697 30.8505494456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.9 0.46 0.884 4.5 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 2A8N 2.40045827641 21.0651823974 1.35523401539 7649 379 99.9477329152 0.190815182497 0.189133278643 0.1894 0.220513679948 0.2197 37.4680633037
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 13.0700643364 f_angle_d 0.681622233086 f_chiral_restr 0.0465316618812 f_bond_d 0.00546655003524 f_plane_restr 0.00241928732814
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1160 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement PHENIX refinement CrysalisPro data reduction SCALA data scaling PHASER phasing