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The crystal structure of the Ras related protein RRas2 (RRAS2) in the GDP bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1R PDB ID 1X1R.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 277 8 % PEG3350, 0.005 M MgCl2, 0.005 M CoCl2, 0.1 M Bis Tris, 0.1 M Mg(Formate)2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.191 α = 90 b = 72.115 β = 90 c = 82.073 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 MARMOSAIC 225 mm CCD 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 98.9 5.8 40966
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 92.7 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 ID 1X1R.PDB 1.7 50 38848 38848 2062 98.9 0.198 0.196 0.2062 0.233 0.1905 RANDOM 18.16
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 3.24 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.775 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_4_deg 12.328 r_dihedral_angle_1_deg 8.911 r_scangle_it 2.292 r_angle_other_deg 1.575 r_scbond_it 1.575 r_angle_refined_deg 1.352 r_mcangle_it 0.997 r_mcbond_it 0.693
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.775 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_4_deg 12.328 r_dihedral_angle_1_deg 8.911 r_scangle_it 2.292 r_angle_other_deg 1.575 r_scbond_it 1.575 r_angle_refined_deg 1.352 r_mcangle_it 0.997 r_mcbond_it 0.693 r_symmetry_vdw_other 0.209 r_nbd_refined 0.193 r_nbd_other 0.179 r_symmetry_vdw_refined 0.178 r_nbtor_refined 0.176 r_mcbond_other 0.162 r_chiral_restr 0.15 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.083 r_metal_ion_refined 0.029 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2688 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing