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Crystal structure of dCas9 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 0.2M Ammonium phosphate dibasic, 20%(w/v) Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.87 57.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.943 α = 90 b = 69.058 β = 110.21 c = 190.046 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 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 98.3 0.061 12.1 6.4 35665
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 97.7 0.393 0.748
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4UN3 3.2 40.89 30136 1564 87.03 0.20075 0.1969 0.27554 0.2424 RANDOM
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] -1.66 2.37 -7.1 5.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.943 r_dihedral_angle_3_deg 23.137 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_1_deg 8.707 r_long_range_B_refined 6.923 r_long_range_B_other 6.923 r_mcangle_it 4.671 r_mcangle_other 4.671 r_scangle_other 4.038 r_mcbond_it 2.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.943 r_dihedral_angle_3_deg 23.137 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_1_deg 8.707 r_long_range_B_refined 6.923 r_long_range_B_other 6.923 r_mcangle_it 4.671 r_mcangle_other 4.671 r_scangle_other 4.038 r_mcbond_it 2.732 r_mcbond_other 2.73 r_scbond_it 2.331 r_scbond_other 2.331 r_angle_refined_deg 1.766 r_angle_other_deg 1.277 r_chiral_restr 0.09 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 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 10758 Nucleic Acid Atoms 2526 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction