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Crystal structure of Rab8 in its inactive GDP-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 All crystals were obtained by mixing 1 ul protein and 1 ul reservoir solution. Crystals of Rab8a6-176:GDP were obtained by mixing of 1 ul protein (20 mg/ml, buffer: 25 mM HEPES pH 7.5, 40 mM NaCl, 1 mM MgCl2, 10 M GDP and 5 mM beta-mercaptoethanol) with 1 ul of reservoir consisting of 16% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES. The crystal was protected with cryo solution containing 30% (w/v) PEG4000, 0.1 M CaAc2, 0.1 M HEPES pH 7.0 before data collection, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.836 α = 90 b = 75.95 β = 98.44 c = 106.618 γ = 90
Symmetry Space Group C 1 2 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 2009-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9786 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 1.95 20 99.2 67917 67378 3.8 19.16
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1YZQ 1.95 19.96 63957 3388 99.28 0.20441 0.20229 0.2136 0.24428 0.2528 RANDOM 36.651
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] 1.04 -0.2 0.56 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.63 r_dihedral_angle_4_deg 16.237 r_dihedral_angle_3_deg 15.796 r_dihedral_angle_1_deg 6.146 r_mcbond_other 4.325 r_angle_other_deg 4.199 r_scangle_it 3.299 r_mcangle_it 2.964 r_scbond_it 2.08 r_mcbond_it 1.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.63 r_dihedral_angle_4_deg 16.237 r_dihedral_angle_3_deg 15.796 r_dihedral_angle_1_deg 6.146 r_mcbond_other 4.325 r_angle_other_deg 4.199 r_scangle_it 3.299 r_mcangle_it 2.964 r_scbond_it 2.08 r_mcbond_it 1.904 r_angle_refined_deg 1.354 r_symmetry_vdw_refined 0.308 r_symmetry_hbond_refined 0.26 r_nbd_other 0.241 r_symmetry_vdw_other 0.24 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.183 r_nbtor_other 0.112 r_metal_ion_refined 0.099 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_other 0.005 r_gen_planes_refined 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6273 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 145
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction SCALEPACK data scaling