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Crystal Structure of Hydra Adenosine Deaminase Acting on RNA (ADAR) Deaminase Domain
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, HANGING DROP 6.5 294 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.4 α = 83.109 b = 49.44 β = 80.171 c = 83.04 γ = 71.06
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 EIGER2 XE 16M 2021-12-11 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) Rrim I (All) 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 1.998 65 95.2 0.094 0.111 0.996 7.79 3.52 47063 -3 34.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 95.1 1.123 1.323 0.737 1.23 3.54
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.998 39.376 47063 2542 94.96 0.213 0.2111 0.2222 0.2429 0.2532 53.135
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] 0.732 1.705 0.885 0.447 1.471 0.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.562 r_dihedral_angle_6_deg 15.514 r_dihedral_angle_2_deg 11.577 r_lrange_other 8.639 r_lrange_it 8.638 r_dihedral_angle_1_deg 6.762 r_mcangle_it 5.027 r_mcangle_other 5.027 r_scangle_it 4.624 r_scangle_other 4.623
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.562 r_dihedral_angle_6_deg 15.514 r_dihedral_angle_2_deg 11.577 r_lrange_other 8.639 r_lrange_it 8.638 r_dihedral_angle_1_deg 6.762 r_mcangle_it 5.027 r_mcangle_other 5.027 r_scangle_it 4.624 r_scangle_other 4.623 r_mcbond_it 2.867 r_mcbond_other 2.865 r_scbond_it 2.845 r_scbond_other 2.845 r_angle_refined_deg 1.672 r_angle_other_deg 0.591 r_nbd_refined 0.22 r_nbd_other 0.22 r_symmetry_nbd_other 0.214 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.144 r_ncsr_local_group_1 0.135 r_symmetry_xyhbond_nbd_refined 0.113 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5481 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing