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Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.204 α = 90 b = 77.089 β = 91.558 c = 58.41 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2019-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.999995 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.92 50 94 0.991 16.33 3 36147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 0.486
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4hdo 1.924 36.514 36123 1772 93.712 0.223 0.2201 0.2219 0.2861 0.29 48.081
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] -0.834 2.847 -1.463 2.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.315 r_dihedral_angle_4_deg 18.472 r_dihedral_angle_3_deg 18.01 r_dihedral_angle_1_deg 7.056 r_lrange_it 6.197 r_mcangle_it 3.309 r_scangle_it 2.768 r_mcbond_it 1.777 r_scbond_it 1.539 r_angle_refined_deg 1.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.315 r_dihedral_angle_4_deg 18.472 r_dihedral_angle_3_deg 18.01 r_dihedral_angle_1_deg 7.056 r_lrange_it 6.197 r_mcangle_it 3.309 r_scangle_it 2.768 r_mcbond_it 1.777 r_scbond_it 1.539 r_angle_refined_deg 1.069 r_nbtor_refined 0.314 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.183 r_xyhbond_nbd_refined 0.128 r_metal_ion_refined 0.096 r_chiral_restr 0.084 r_gen_planes_refined 0.004 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3809 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing