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Crystal structure of GDP-bound Rab8:GRAB
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 5.3 293 1.6 M ammonium sulphate and sodium acetate. cryo solution containing 20% glycerol in the reservoir solution, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.53 72.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.93 α = 90 b = 160.38 β = 90 c = 166.51 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 48.21 99.6 19050 21124 7.6 9.9
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 3.3 48.21 21124 1140 97.99 0.24643 0.24419 0.2523 0.28962 0.2923 RANDOM 96.488
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] 15.72 -5.55 -10.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.625 r_dihedral_angle_3_deg 23.693 r_dihedral_angle_4_deg 17.315 r_mcangle_it 6.274 r_dihedral_angle_1_deg 6.158 r_scbond_it 3.694 r_mcbond_it 3.668 r_mcbond_other 3.666 r_angle_refined_deg 1.497 r_angle_other_deg 0.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.625 r_dihedral_angle_3_deg 23.693 r_dihedral_angle_4_deg 17.315 r_mcangle_it 6.274 r_dihedral_angle_1_deg 6.158 r_scbond_it 3.694 r_mcbond_it 3.668 r_mcbond_other 3.666 r_angle_refined_deg 1.497 r_angle_other_deg 0.823 r_symmetry_vdw_refined 0.25 r_xyhbond_nbd_refined 0.199 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other 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 4807 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose MOSFLM data reduction PHASES phasing REFMAC refinement XDS data reduction SCALEPACK data scaling