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Human Rab8a phosphorylated at Ser111 in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.55 α = 90 b = 75.18 β = 100.48 c = 107.7 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 PIXEL DECTRIS EIGER X 16M 2018-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.4 50 97.2 0.096 9.5 3 35267
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 96.9 0.574 2.1
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 4LHV 2.4 30 33488 1763 97.17 0.2343 0.2328 0.2454 0.2623 0.2698 RANDOM 48.379
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] -0.46 1.04 0.01 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.784 r_dihedral_angle_4_deg 16.246 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_1_deg 6.443 r_angle_refined_deg 1.224 r_angle_other_deg 1.05 r_rigid_bond_restr 0.187 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.784 r_dihedral_angle_4_deg 16.246 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_1_deg 6.443 r_angle_refined_deg 1.224 r_angle_other_deg 1.05 r_rigid_bond_restr 0.187 r_chiral_restr 0.034 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6685 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing