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Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFK 2DFK, 5D3W experimental model PDB 5D3W 2DFK, 5D3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 Ammonium citrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.46 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.31 α = 90 b = 95.906 β = 90 c = 277.131 γ = 90
Symmetry Space Group C 2 2 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 2013-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9788 APS 21-ID-D
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 3.16 50 83.6 0.071 8.3 3.5 12403 83.61
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 3.16 3.21 87.2 0.446 3.6 584
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DFK, 5D3W 3.203 43.122 1.36 12360 622 81.22 0.208 0.2048 0.216 0.198 0.1996 RANDOM 124.726
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 13.747 f_angle_d 0.706 f_chiral_restr 0.025 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4194 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction SCALEPACK data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction