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Crystal structure of Kalirin/Rac1 in complex with RS-009
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M bis-tris pH 5.5, 0.1 M NaCl,
27% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.371 α = 90 b = 62.371 β = 90 c = 339.355 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2019-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.68 56.56 100 0.121 0.991 12 17.6 46349 27.44
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 1.68 1.72 0.789
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.68 56.56 1.38 46172 2247 99.97 0.2447 0.2434 0.2453 0.2693 0.2718 31.17
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.7726 f_angle_d 0.8571 f_chiral_restr 0.0515 f_bond_d 0.0065 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2633 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing