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Crystal structure of an anti-CRISPR Protein AcrIE7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9N3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 22% PEG MME 5K, 0.1M BisTris (pH 5.4)
Crystal Properties Matthews coefficient Solvent content 2.31 46.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.501 α = 90 b = 62.077 β = 103.208 c = 87.737 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 90 PIXEL DECTRIS EIGER X 16M 2023-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.034 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 1.5 85.42 98.7 0.073 0.075 0.018 0.999 21.8 32.7 51688 32.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 98.7 2.813 2.88 0.604 0.696 1.2 21.5
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 1.5 85.416 51687 2590 98.632 0.208 0.2065 0.2066 0.2368 0.237 39.393
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] -1.406 0.302 0.412 0.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.932 r_dihedral_angle_3_deg 14.021 r_dihedral_angle_2_deg 9.54 r_lrange_other 6.813 r_lrange_it 6.809 r_scangle_it 6.221 r_scangle_other 6.22 r_dihedral_angle_1_deg 5.44 r_scbond_it 4.453 r_scbond_other 4.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.932 r_dihedral_angle_3_deg 14.021 r_dihedral_angle_2_deg 9.54 r_lrange_other 6.813 r_lrange_it 6.809 r_scangle_it 6.221 r_scangle_other 6.22 r_dihedral_angle_1_deg 5.44 r_scbond_it 4.453 r_scbond_other 4.435 r_mcangle_it 3.231 r_mcangle_other 3.23 r_mcbond_it 2.843 r_mcbond_other 2.835 r_angle_refined_deg 2.18 r_angle_other_deg 0.738 r_nbd_refined 0.238 r_nbd_other 0.208 r_symmetry_nbd_refined 0.195 r_nbtor_refined 0.192 r_symmetry_nbd_other 0.184 r_xyhbond_nbd_refined 0.132 r_ncsr_local_group_2 0.131 r_chiral_restr 0.118 r_symmetry_xyhbond_nbd_refined 0.113 r_ncsr_local_group_3 0.113 r_ncsr_local_group_1 0.104 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.016 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 2506 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 1
Software Software Software Name Purpose Coot model building REFMAC refinement PHASER phasing Aimless data scaling pointless data scaling DIALS data reduction Blu-Ice data collection