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Crystal structure of RNase T in complex with a preferred ssDNA (TAGG) with two Mg in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGY PDB ENTRY 3NGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.1M MES monohydrate pH 6.0, 20% w/v PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.767152 30.396488
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.482 α = 90 b = 46.482 β = 90 c = 315.877 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 0.999 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 2.1 30 99.5 0.056 24.2 3.2 43799 43799
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 2.1 2.18 99.4 0.269 4.7 3.1 4281
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB ENTRY 3NGY 2.107 23.377 1.99 43731 43731 3383 99.21 0.1937 0.175 0.1706 0.168 0.2286 0.2256 RANDOM 31.0035
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] -0.0943 -0.0943 0.1887
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.706 f_angle_d 1.012 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6359 Nucleic Acid Atoms 321 Solvent Atoms 343 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling