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Crystal Structure of anti-CRISPR AcrIE7 Determined by Experimental MAD Phasing with Hg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1.5M Na Malonate (pH 8.0), 0.1M HEPES (pH 7.5)
Crystals soaked in Mother Liquor containing 1mM HgCl2 overnight before backsoaking in cryoprotectant (2.6M Na Malonate) and plunge freezing
Crystal Properties Matthews coefficient Solvent content 4.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.102 α = 90 b = 108.102 β = 90 c = 187.713 γ = 120
Symmetry Space Group P 63 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 90 PIXEL DECTRIS EIGER X 16M 2023-04-23 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9753, 1.0070, 1.0088, 1.0108 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.198 49.95 99.9 0.334 0.342 0.073 0.998 15.3 39.8 33732 16.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 99.4 1.63 0.79 2.19
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 MAD FREE R-VALUE 2.198 46.928 33731 1784 99.825 0.193 0.1907 0.1927 0.2268 0.228 29.175
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] 0.421 0.21 0.421 -1.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.598 r_dihedral_angle_3_deg 15.704 r_dihedral_angle_2_deg 14.849 r_lrange_other 6.316 r_lrange_it 6.307 r_dihedral_angle_1_deg 5.831 r_scangle_it 4.795 r_scangle_other 4.793 r_scbond_it 3.188 r_scbond_other 3.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.598 r_dihedral_angle_3_deg 15.704 r_dihedral_angle_2_deg 14.849 r_lrange_other 6.316 r_lrange_it 6.307 r_dihedral_angle_1_deg 5.831 r_scangle_it 4.795 r_scangle_other 4.793 r_scbond_it 3.188 r_scbond_other 3.132 r_mcangle_other 3.124 r_mcangle_it 3.123 r_angle_refined_deg 2.434 r_mcbond_it 2.101 r_mcbond_other 2.096 r_angle_other_deg 0.818 r_metal_ion_refined 0.332 r_nbd_refined 0.243 r_symmetry_xyhbond_nbd_refined 0.215 r_nbtor_refined 0.198 r_symmetry_nbd_other 0.185 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.125 r_chiral_restr 0.109 r_ncsr_local_group_1 0.108 r_ncsr_local_group_3 0.103 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_2 0.069 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2524 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling pointless data scaling SHELXCD phasing SHELXDE phasing Blu-Ice data collection Coot model building