☰ Navigation Tabs
Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M MES:NaOH pH 6.5, 14% PEG 20,000
Crystal Properties Matthews coefficient Solvent content 2.6 57.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.68 α = 90 b = 63.44 β = 126.64 c = 132.06 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 PIXEL DECTRIS PILATUS 6M 2017-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.55 106 97.4 0.063 0.998 15.27 3.44 37329
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.62 98.1 0.723 0.736 2.07 3.5
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 1ZY7 2.55 105.96 35463 1862 97.67 0.19334 0.19012 0.1957 0.25518 0.2538 RANDOM 64.39
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] 2.05 1.2 -4.83 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_4_deg 20.478 r_dihedral_angle_3_deg 16.634 r_long_range_B_refined 9.171 r_long_range_B_other 9.171 r_dihedral_angle_1_deg 7.166 r_scangle_other 7.055 r_mcangle_it 7.002 r_mcangle_other 7.001 r_scbond_it 4.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.143 r_dihedral_angle_4_deg 20.478 r_dihedral_angle_3_deg 16.634 r_long_range_B_refined 9.171 r_long_range_B_other 9.171 r_dihedral_angle_1_deg 7.166 r_scangle_other 7.055 r_mcangle_it 7.002 r_mcangle_other 7.001 r_scbond_it 4.817 r_scbond_other 4.815 r_mcbond_it 4.698 r_mcbond_other 4.695 r_angle_refined_deg 1.739 r_angle_other_deg 1.101 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5760 Nucleic Acid Atoms 967 Solvent Atoms 48 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing