☰ Navigation Tabs
Crystal structure and RNA binding properties of the RRM/AlkB domains in human ABH8, an enzyme catalyzing tRNA hypermodification, Northeast Structural Genomics Consortium Target HR5601B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3THP PDB entry 3THP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 5.6 293 2.8 mM Mn2Cl and 8.6 mM 2OG and a precipitant containing 28.5-30.5% (w/v) PEG 4K, 15% (v/v) glycerol, 170 mM NH4(CH3COO), 85 mM Na-citrate, pH 5.6, microbatch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.166 α = 90 b = 73.279 β = 112.73 c = 149.814 γ = 90
Symmetry Space Group C 1 2 1
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 4 mirrors 2010-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97912 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3 40 99.5 0.082 0.071 16.4 3.5 30026 29876 44.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 98.6 0.304 0.272 3.7 3.4 2993
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3THP 3.01 39.06 30026 29071 2904 96.2 0.224 0.22 0.22 0.2196 0.277 0.2776 RANDOM 48.7
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] -10.63 1.64 15.57 -4.93
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_angle_deg 1.2 c_improper_angle_d 0.77 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9610 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 48
Software Software Software Name Purpose ADSC data collection MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling