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Crystal structure of xCas9 in complex with sgRNA and DNA (TGA PAM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 0.2 M Ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.005 α = 90 b = 70.314 β = 110.34 c = 190.077 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 85 CCD AGILENT EOS CCD 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.2 50 99 0.08 0.995 10.2 4.8 36568
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 98.9 0.613 0.548 4.3
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 4UN3 3.2 49.38 28597 1564 81.8 0.22308 0.21982 0.2215 0.28201 0.2779 RANDOM 76.627
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] -1.86 0.65 -3.39 3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 20.4 r_dihedral_angle_4_deg 18.474 r_dihedral_angle_1_deg 8.144 r_long_range_B_refined 6.863 r_long_range_B_other 6.863 r_mcangle_it 4.857 r_mcangle_other 4.857 r_scangle_other 3.407 r_mcbond_it 2.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 20.4 r_dihedral_angle_4_deg 18.474 r_dihedral_angle_1_deg 8.144 r_long_range_B_refined 6.863 r_long_range_B_other 6.863 r_mcangle_it 4.857 r_mcangle_other 4.857 r_scangle_other 3.407 r_mcbond_it 2.796 r_mcbond_other 2.793 r_scbond_it 1.893 r_scbond_other 1.893 r_angle_refined_deg 1.649 r_angle_other_deg 1.265 r_chiral_restr 0.076 r_bond_refined_d 0.008 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 10326 Nucleic Acid Atoms 2488 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing