☰ Navigation Tabs
Crystal structure of human Rab38 in complex with GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288 Morpheus A9
10% PEG 20000
20% PEG 550 MME
0.02M divalent cations
0.1M bicine/Trizma base pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.045 α = 90 b = 70.993 β = 102.21 c = 74.487 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 PIXEL DECTRIS EIGER X 9M 2018-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.79 49.28 98.7 0.075 0.082 12.9 6.8 66651
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 0.652 0.718
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ff8 1.793 49.28 1.84 66457 3358 99.08 0.1897 0.1884 0.1919 0.2123 0.2153
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 f_dihedral_angle_d 10.491 f_angle_d 0.796 f_chiral_restr 0.054 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5517 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing