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The crystal structure of Arabidopsis thaliana RAC7-ROP9: the first RAS superfamily GTPase from the plant kingdom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MH1 PDB ENTRY 1MH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 50 MM BISTRIS PH 6.5, 10 MM MGCL2, 5 MM DTT, 200 MM KCL, 10% (W/V) PEG 2000, 10% (W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.9 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.76 α = 90 b = 30.2 β = 100.06 c = 139.36 γ = 90
Symmetry Space Group P 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 MARRESEARCH 2005-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.78 38.18 100 0.08 12.3 4.1 61628 16.88
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 1.78 1.88 100 0.44 3.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT PDB ENTRY 1MH1 1.78 37.8 58521 3106 100 0.189 0.187 0.1865 0.227 0.2267 RANDOM 19.73
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] -0.45 -0.29 -0.42 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.157 r_dihedral_angle_4_deg 17.1 r_dihedral_angle_3_deg 14.723 r_dihedral_angle_1_deg 6.276 r_scangle_it 3.825 r_scbond_it 2.543 r_mcangle_it 1.789 r_angle_refined_deg 1.633 r_mcbond_it 1.16 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.157 r_dihedral_angle_4_deg 17.1 r_dihedral_angle_3_deg 14.723 r_dihedral_angle_1_deg 6.276 r_scangle_it 3.825 r_scbond_it 2.543 r_mcangle_it 1.789 r_angle_refined_deg 1.633 r_mcbond_it 1.16 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.252 r_symmetry_hbond_refined 0.217 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.119 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5375 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing