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Crystal structure of geranylgeranylated RhoA in complex with RhoGDI in its active GPPNHP-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DOA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 20% (w/v) PEG 3350, 0.2M MgCl2, 0.1M Hepes-NaOH, 25mM Hepes-NaOH pH 7.2, 40mM NaCl, 3mM MgCl2, 10M GMPPNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46 α = 90 b = 71.576 β = 90 c = 136.03 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 100 CCD ADSC QUANTUM 210 2011-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 68.01 97 0.069 0.07 12.33 2.7 21383 20741 6.9 12.33 41.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 98.1 0.265 0.279 3.6 2.7 2156
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1DOA 2.8 68.01 3.6 3.6 21383 20741 544 98.86 0.206 0.20579 0.202 0.2008 0.28133 0.2736 RANDOM 37.387
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] 2.09 -1.86 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.079 r_dihedral_angle_3_deg 23.045 r_dihedral_angle_4_deg 20.555 r_dihedral_angle_1_deg 7.704 r_scangle_it 3.696 r_scbond_it 2.095 r_angle_refined_deg 1.743 r_mcangle_it 1.415 r_mcbond_it 0.716 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.079 r_dihedral_angle_3_deg 23.045 r_dihedral_angle_4_deg 20.555 r_dihedral_angle_1_deg 7.704 r_scangle_it 3.696 r_scbond_it 2.095 r_angle_refined_deg 1.743 r_mcangle_it 1.415 r_mcbond_it 0.716 r_chiral_restr 0.117 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2992 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 54
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement XDS data reduction XSCALE data scaling