☰ Navigation Tabs
The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ERX PDB ENTRY 2ERX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 3.5 M Sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.053 α = 90 b = 94.031 β = 89.98 c = 61.214 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 MARMOSAIC 225 mm CCD 2006-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9789 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 1.9 50 97.7 55909 55909
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 99.2
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 (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 PDB ENTRY 2ERX 1.9 47.09 54127 54127 1661 97.65 0.16128 0.16128 0.15987 0.1832 0.20781 0.2233 RANDOM 20.224
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] -0.1 0.02 0.08 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.268 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 7.763 r_scangle_it 7.049 r_scbond_it 5.067 r_mcangle_it 3.204 r_mcbond_it 2.667 r_angle_refined_deg 1.398 r_angle_other_deg 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.268 r_dihedral_angle_4_deg 16.11 r_dihedral_angle_3_deg 12.626 r_dihedral_angle_1_deg 7.763 r_scangle_it 7.049 r_scbond_it 5.067 r_mcangle_it 3.204 r_mcbond_it 2.667 r_angle_refined_deg 1.398 r_angle_other_deg 0.922 r_mcbond_other 0.794 r_symmetry_vdw_other 0.276 r_xyhbond_nbd_refined 0.23 r_nbd_refined 0.213 r_nbd_other 0.203 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.173 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.083 r_nbtor_other 0.083 r_metal_ion_refined 0.022 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5447 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing