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Crystal structure of GTP-bound Rab8:Rabin8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZQ PDB ENTRY 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 hours at 278 K, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.59 65.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.337 α = 90 b = 165.561 β = 90 c = 167.263 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 1.0000 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 3.2 20 99.4 19050 18932 9.9 9.54
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 PDB ENTRY 1YZQ 3.2 19.99 17905 954 99.53 0.27918 0.27761 0.2689 0.30877 0.2986 RANDOM 92.122
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] 4.28 2.11 -6.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.704 r_dihedral_angle_3_deg 23.436 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_1_deg 7.52 r_angle_other_deg 4.439 r_scangle_it 3.415 r_scbond_it 2.118 r_mcangle_it 1.995 r_angle_refined_deg 1.639 r_mcbond_it 1.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.704 r_dihedral_angle_3_deg 23.436 r_dihedral_angle_4_deg 21.853 r_dihedral_angle_1_deg 7.52 r_angle_other_deg 4.439 r_scangle_it 3.415 r_scbond_it 2.118 r_mcangle_it 1.995 r_angle_refined_deg 1.639 r_mcbond_it 1.095 r_mcbond_other 1.082 r_nbd_refined 0.268 r_symmetry_vdw_other 0.25 r_nbd_other 0.24 r_nbtor_refined 0.203 r_symmetry_vdw_refined 0.192 r_xyhbond_nbd_refined 0.161 r_nbtor_other 0.114 r_xyhbond_nbd_other 0.106 r_chiral_restr 0.076 r_symmetry_hbond_refined 0.056 r_bond_refined_d 0.016 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_mcangle_other r_scbond_other 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 4735 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction SCALEPACK data scaling