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Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C1Y PDB ENTRY 1C1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 278 15% PEG2000 MME, 100 mM Tris, 100 mM potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.35 47.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.85 α = 90 b = 77.75 β = 91.2 c = 58.85 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 315 2010-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.67 50 96 0.046 31.27 3.6 57913 57913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.77 80 0.35 4.37 2.8 21549
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-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 PDB ENTRY 1C1Y 1.67 32.43 55017 2896 96 0.21253 0.21253 0.21153 0.2161 0.23142 0.2302 RANDOM 19.771
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] -0.84 0.32 0.62 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 14.367 r_dihedral_angle_3_deg 13.619 r_dihedral_angle_1_deg 5.666 r_angle_refined_deg 1.006 r_angle_other_deg 0.768 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 14.367 r_dihedral_angle_3_deg 13.619 r_dihedral_angle_1_deg 5.666 r_angle_refined_deg 1.006 r_angle_other_deg 0.768 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3830 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 39
Software Software Software Name Purpose dls data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling