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Crystal Structure of Guanine Nucleotide-Binding Protein Alpha Subunit (G Protein) from Oryza sativa in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Phyre2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 200 mM sodium acetate trihydrate (pH 8.5), 100 mM Tris (pH 8.5), 30% (w/v) PEG-4000
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.393 α = 90 b = 68.419 β = 89.91 c = 167.977 γ = 90
Symmetry Space Group P 1 21 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 315 2014-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.99 50 99.9 0.036 0.061 0.031 26.44 3.8 31650
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.99 3.04 0.512 0.711 0.362 0.744 1.94
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 2.99 48.37 5.38 30214 2079 95.22 0.269 0.266 0.243 0.3061 0.2755 95.83
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 9.4777 f_angle_d 1.0911 f_chiral_restr 0.0527 f_plane_restr 0.0058 f_bond_d 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9801 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 116
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection PHASER phasing Coot model building HKL-3000 data reduction HKL-3000 data scaling