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Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2
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 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.11 α = 90 b = 76.83 β = 92.281 c = 58.21 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 2017-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976484 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 46.4 98.6 0.046 0.999 16.49 3.78 42373
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 1.406 0.78
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 1.85 46.374 42373 2119 98.592 0.247 0.2444 0.2438 0.2923 0.2915 52.232
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] -0.026 -0.073 0.19 -0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.554 r_dihedral_angle_4_deg 20.275 r_dihedral_angle_3_deg 19.141 r_lrange_it 7.276 r_dihedral_angle_1_deg 6.756 r_mcangle_it 4.165 r_scangle_it 3.902 r_mcbond_it 2.431 r_scbond_it 2.327 r_angle_refined_deg 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.554 r_dihedral_angle_4_deg 20.275 r_dihedral_angle_3_deg 19.141 r_lrange_it 7.276 r_dihedral_angle_1_deg 6.756 r_mcangle_it 4.165 r_scangle_it 3.902 r_mcbond_it 2.431 r_scbond_it 2.327 r_angle_refined_deg 1.19 r_symmetry_xyhbond_nbd_refined 0.446 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.092 r_metal_ion_refined 0.057 r_gen_planes_refined 0.005 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3835 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing