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Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NX8 PDB entry 2NX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.53 α = 90 b = 103.12 β = 97.6 c = 77.59 γ = 90
Symmetry Space Group P 1 21 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 315 Mirrors 2008-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.28130 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.8 20 99.7 0.137 12.64 7.2 18343 18284 -3 25.535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 99.7 0.746 3.88 6.84 1802
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2NX8 2.8 20 17318 912 100 0.20502 0.20237 0.2075 0.25614 0.261 RANDOM 25.535
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] -2.81 -1.36 5.42 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.953 r_dihedral_angle_3_deg 17.741 r_dihedral_angle_4_deg 9.05 r_dihedral_angle_1_deg 5.762 r_scangle_it 1.684 r_angle_refined_deg 1.419 r_scbond_it 1.219 r_angle_other_deg 1.062 r_mcbond_it 0.675 r_mcangle_it 0.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.953 r_dihedral_angle_3_deg 17.741 r_dihedral_angle_4_deg 9.05 r_dihedral_angle_1_deg 5.762 r_scangle_it 1.684 r_angle_refined_deg 1.419 r_scbond_it 1.219 r_angle_other_deg 1.062 r_mcbond_it 0.675 r_mcangle_it 0.665 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.197 r_symmetry_vdw_other 0.194 r_nbtor_refined 0.182 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.138 r_mcbond_other 0.11 r_nbtor_other 0.09 r_chiral_restr 0.087 r_metal_ion_refined 0.061 r_bond_other_d 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5043 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling PHASER phasing