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Crystal structure of RNase T in complex with a preferred ssDNA (TTA) with two Mg in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 6%(v/v) Tacsimate, 0.1M MES monohydrate, 25%(w/v) Polyethylene glycol 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.8 31.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.34 α = 90 b = 46.34 β = 90 c = 315.354 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 315 2010-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 0.9999 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.7 30 97.3 0.0054 23.91 2.6 80910 80910
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.7 0.352 3.03 2.7 8190
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3NGY 1.702 26.394 1.97 80817 80817 6243 97.29 0.1944 0.1944 0.1918 0.1915 0.2262 0.2257 RANDOM 25.2441
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] 1.0907 1.0907 -2.1814
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.679 f_angle_d 0.872 f_chiral_restr 0.063 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6282 Nucleic Acid Atoms 244 Solvent Atoms 804 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling