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Crystal structure of xCas9 in complex with sgRNA and DNA (TGC 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 2.92 57.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.464 α = 90 b = 70.364 β = 110.42 c = 188.899 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 50 98.8 0.071 1 12 6.5 43368
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 3.11 96.9 0.578 0.543 5.5
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 3.01 49.25 36346 1905 86.98 0.23934 0.23691 0.237 0.28531 0.2829 RANDOM 70.805
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] 0.15 -1.16 -1.56 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_3_deg 18.942 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_1_deg 7.257 r_long_range_B_refined 5.866 r_long_range_B_other 5.866 r_mcangle_it 4.124 r_mcangle_other 4.124 r_scangle_other 2.92 r_mcbond_it 2.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.986 r_dihedral_angle_3_deg 18.942 r_dihedral_angle_4_deg 18.491 r_dihedral_angle_1_deg 7.257 r_long_range_B_refined 5.866 r_long_range_B_other 5.866 r_mcangle_it 4.124 r_mcangle_other 4.124 r_scangle_other 2.92 r_mcbond_it 2.384 r_mcbond_other 2.384 r_angle_refined_deg 1.659 r_scbond_it 1.63 r_scbond_other 1.63 r_angle_other_deg 1.359 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 9924 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