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Crystal structure of GDP-bound Rab1a-T75D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 291.15 40mM Lithium chloride, 20mM Magnesium chloride hexahydrate, 80mM NaCl, 2mM Hexammine cobalt(III) chloride, 40mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.489 α = 76.945 b = 50.598 β = 84.616 c = 52.626 γ = 86.271
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 315r 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.977760 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5509 25.12 95.2 0.059 42.71 3.7 54416 12.5307915404
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5509 1.61 0.539
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 2FOL 1.55090284637 25.1160419845 1.9676416371 54114 2740 94.5883586786 0.161457428126 0.160166333291 0.1603 0.185187062179 0.1858 19.7969176503
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 10.1516128269 f_angle_d 0.902373057224 f_chiral_restr 0.0557843004204 f_bond_d 0.00557696811916 f_plane_restr 0.004119644021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2775 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing