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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 2CQ2 PDB entry 2CQ2 for RRM domain, PDB entry 2FDI for AlkB domain. experimental model PDB 2FDI PDB entry 2CQ2 for RRM domain, PDB entry 2FDI for AlkB domain.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7 293 30% PEG 3350 and 0.15 M D/L malic acid, 2.8 mM MnCl2, and 8.6 mM 2-oxyglutarate., pH 7, microbatch under oil, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.276 α = 90 b = 81.675 β = 90 c = 144.72 γ = 90
Symmetry Space Group I 2 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 CCD MAR CCD 165 mm mirrors 2010-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.97885 NSLS X4C
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 3.2 40 99.9 0.154 0.124 14.3 7.4 12782 12770 42.5
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 3.2 3.31 99.6 0.437 0.393 3.7 6.4 1293
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 2CQ2 for RRM domain, PDB entry 2FDI for AlkB domain. 3.2 35.57 12782 12202 1210 94.9 0.22 0.217 0.217 0.2298 0.283 0.2832 RANDOM 44.2
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] -12.99 24.43 -11.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_angle_deg 1.1 c_improper_angle_d 0.76 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2413 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose ADSC data collection PHASER phasing CNS refinement DENZO data reduction SCALEPACK data scaling