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Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WM9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.2M Potassium phosphate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.185 α = 90 b = 73.279 β = 104.82 c = 65.031 γ = 90
Symmetry Space Group C 1 2 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 210 2010-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.085 30 99.5 0.06 24.6 5.5 28080 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.16 98.4 0.338 4.96 5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2WM9 2.085 29.679 26517 1905 93.68 0.1823 0.1785 0.1731 0.2324 0.2253 RANDOM
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] -3.3048 7.3091 0.2683 3.0365
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.217 f_angle_d 1.275 f_chiral_restr 0.1 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3577 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX model building PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing