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Crystal structure of GDP-bound Rab8:Rabin8
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 6.6 293 Nucleotide-free Rab8a1 184:Rabin8157-232 was crystallized in 18% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6. Before data collection, the complex crystal was protected with cryo solution (30% (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6). In order to produce nucleotide-bound forms of Rab8:Rabin8 complexes, the nucleotide-free Rab8:Rabin8 crystals were soaked with cryo solution containing 30 % (w/v) PEG3350, 0.1 M Li2SO4, 0.1 M MES pH 6.6 and 1 mM respective nucleotide GDP/GTP for one hour at 4 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.52 65.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.587 α = 90 b = 164.765 β = 90 c = 166.421 γ = 90
Symmetry Space Group C 2 2 21
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 0.9840 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 3.1 20.1 98 20523 20118 8.3 13.56
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 3.1 20.08 19035 1003 98.11 0.28957 0.28848 0.2841 0.31031 0.3079 RANDOM 89.471
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] 2.68 3.74 -6.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.275 r_dihedral_angle_3_deg 23.421 r_dihedral_angle_4_deg 22.287 r_dihedral_angle_1_deg 7.651 r_angle_other_deg 4.425 r_angle_refined_deg 1.708 r_symmetry_hbond_refined 0.531 r_nbd_refined 0.27 r_symmetry_vdw_other 0.264 r_nbd_other 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.275 r_dihedral_angle_3_deg 23.421 r_dihedral_angle_4_deg 22.287 r_dihedral_angle_1_deg 7.651 r_angle_other_deg 4.425 r_angle_refined_deg 1.708 r_symmetry_hbond_refined 0.531 r_nbd_refined 0.27 r_symmetry_vdw_other 0.264 r_nbd_other 0.24 r_symmetry_vdw_refined 0.231 r_nbtor_refined 0.201 r_xyhbond_nbd_refined 0.182 r_nbtor_other 0.117 r_xyhbond_nbd_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4727 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 61
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction SCALEPACK data scaling