6KC8

Crystal structure of WT Nme1Cas9 in complex with sgRNA and target DNA (ATATGATT PAM) in post-cleavage state


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.228919% PEG 3350, 0.2M Na citrate, 0.1M Bis-Tris propane pH 7.2
Crystal Properties
Matthew coefficientSolvent content
3.3363.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.604α = 90
b = 159.517β = 90
c = 117.963γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-06-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97918SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.95099.80.2070.2220.0790.98612.9756256
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.9599.70.9691.0560.4090.1121.65.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6JDV2.949.3544188242282.720.20560.202780.25693RANDOM66.414
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]
1.40.14-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.229
r_dihedral_angle_4_deg20.569
r_dihedral_angle_3_deg19.643
r_long_range_B_other17.021
r_long_range_B_refined17.021
r_mcangle_it10.545
r_mcangle_other10.544
r_scangle_other9.668
r_dihedral_angle_1_deg8.515
r_mcbond_other6.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.229
r_dihedral_angle_4_deg20.569
r_dihedral_angle_3_deg19.643
r_long_range_B_other17.021
r_long_range_B_refined17.021
r_mcangle_it10.545
r_mcangle_other10.544
r_scangle_other9.668
r_dihedral_angle_1_deg8.515
r_mcbond_other6.66
r_mcbond_it6.659
r_scbond_it6.04
r_scbond_other6.04
r_angle_refined_deg1.552
r_angle_other_deg1.375
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.002
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8095
Nucleic Acid Atoms3691
Solvent Atoms8
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing