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Crystal structure of the Cas12i1-crRNA binary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.1 M sodium citrate (pH 5.2),
17% (w/v) Polyethylene glycol 3350,
2% Tacsimate (pH 4.0),
0.15 M sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 3.73 67.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.933 α = 90 b = 211.933 β = 90 c = 164.758 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 100 CCD ADSC QUANTUM 315r 2020-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9792 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.6 57.42 99.9 0.998 12.3 38.6 25821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.85 0.955
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 7D2L 3.6 57.42 24504 1290 99.85 0.2815 0.28 0.2854 0.3085 0.3162 RANDOM 144.549
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] 5.58 2.79 5.58 -18.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.039 r_dihedral_angle_3_deg 29.249 r_dihedral_angle_4_deg 26.604 r_dihedral_angle_1_deg 3.84 r_angle_refined_deg 1.09 r_angle_other_deg 0.898 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.039 r_dihedral_angle_3_deg 29.249 r_dihedral_angle_4_deg 26.604 r_dihedral_angle_1_deg 3.84 r_angle_refined_deg 1.09 r_angle_other_deg 0.898 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8557 Nucleic Acid Atoms 871 Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHENIX phasing