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Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D5C PDB entry 1D5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100mM TrisHCl, 1M LiCl, 32% (w/v) polyethylene glycol 1000, 3.3mM Nonyl-D-glucoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.008 α = 90 b = 124.853 β = 107.57 c = 66.162 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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0398 ESRF ID14-4
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 1.82 19.05 87.7 0.056 0.032 17.44 1.9 48538 48538 25.99
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) 1.82 1.9 52.2 0.249 0.146 4.3 3482
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 1D5C 1.82 19.05 46121 46121 2428 100 0.20849 0.20849 0.20484 0.2075 0.27735 0.2759 RANDOM 26.728
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 r_dihedral_angle_2_deg 36.997 r_dihedral_angle_4_deg 20.478 r_dihedral_angle_3_deg 15.831 r_dihedral_angle_1_deg 5.799 r_scangle_it 2.835 r_scbond_it 1.894 r_angle_refined_deg 1.4 r_mcangle_it 1.343 r_mcbond_it 0.814 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.997 r_dihedral_angle_4_deg 20.478 r_dihedral_angle_3_deg 15.831 r_dihedral_angle_1_deg 5.799 r_scangle_it 2.835 r_scbond_it 1.894 r_angle_refined_deg 1.4 r_mcangle_it 1.343 r_mcbond_it 0.814 r_nbtor_refined 0.306 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.088 r_metal_ion_refined 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5194 Nucleic Acid Atoms Solvent Atoms 739 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement ProDC data collection XDS data scaling AMoRE phasing