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Crystal Structure of the P-Rex1 DH/PH tandem in complex with Rac1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFK 2DFK and 5D3W experimental model PDB 5D3W 2DFK and 5D3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 294 Sodium dihydrogen phosphate, PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.373 α = 90 b = 107.053 β = 90 c = 323.568 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.127 APS 21-ID-D
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 3.25 35 98 0.173 0.19 0.076 5.6 5.8 42862 67.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.31 91.9 0.87 0.952 0.377 0.775 5.5 1997
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2DFK and 5D3W 3.282 34.847 1.34 42775 2104 96.81 0.1924 0.1902 0.1963 0.2355 0.2372 81.2588
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 15.568 f_angle_d 1.048 f_chiral_restr 0.044 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16711 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling SCALEPACK data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction