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Crystal structure of Kalirin/Rac1 in complex with MC-278.
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 293 0.1 M citrate pH 4.2, 0.2 M NaCl and 18 % PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.3 46.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.053 α = 90 b = 62.053 β = 90 c = 339.439 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 EIGER2 XE 16M 2022-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.48 56.57 99.8 0.11 0.112 0.019 17.2 30.9 65984 21.12
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 1.48 1.51 0.287
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 1.48 56.57 1.33 65303 3242 98.78 0.2075 0.2061 0.2067 0.2311 0.2329 23.55
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 12.2143 f_angle_d 0.7932 f_chiral_restr 0.0763 f_plane_restr 0.0067 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2680 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction xia2 data scaling PHENIX phasing