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Crystal structure of dCas9 in complex with sgRNA and DNA (CGA 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 0.2M Ammonium phosphate dibasic, 20%(w/v) Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.86 56.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.956 α = 90 b = 69.137 β = 110.34 c = 189.243 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 2019-03-15 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 2.98 50 98.8 0.046 0.989 16.2 6.4 44046
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 2.98 3.09 97.2 0.39 0.793 2 5.7
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 2.98 48.89 38952 2067 91.99 0.20088 0.19703 0.2037 0.27412 0.2702 RANDOM 57.358
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] -0.25 0.24 -2.78 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.935 r_dihedral_angle_3_deg 22.712 r_dihedral_angle_4_deg 21.01 r_dihedral_angle_1_deg 8.806 r_long_range_B_refined 7.062 r_long_range_B_other 7.062 r_mcangle_it 4.846 r_mcangle_other 4.846 r_scangle_other 4.218 r_mcbond_it 2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.935 r_dihedral_angle_3_deg 22.712 r_dihedral_angle_4_deg 21.01 r_dihedral_angle_1_deg 8.806 r_long_range_B_refined 7.062 r_long_range_B_other 7.062 r_mcangle_it 4.846 r_mcangle_other 4.846 r_scangle_other 4.218 r_mcbond_it 2.914 r_mcbond_other 2.906 r_scbond_it 2.497 r_scbond_other 2.497 r_angle_refined_deg 1.833 r_angle_other_deg 1.339 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.004 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 10754 Nucleic Acid Atoms 2526 Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction