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Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KY3 PDB entry 1ky3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 PEG8000, Na-benzoate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.17 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.245 α = 90 b = 98.245 β = 90 c = 79.66 γ = 90
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 MARRESEARCH 2003-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.0091 EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.77 30 99.9 0.053 24.8 3.8 37662 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.77 1.83 99.9 0.0691 2.5 3.8 3752
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 FREE R PDB entry 1ky3 1.77 30 35770 35770 1825 99.9 0.1646 0.1583 0.2213 0.2069 keep twin-related reflection in same set 30
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 4 2550 3027.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.08 s_non_zero_chiral_vol 0.039 s_zero_chiral_vol 0.033 s_from_restr_planes 0.0255 s_angle_d 0.023 s_anti_bump_dis_restr 0.017 s_bond_d 0.007 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2712 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 96
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling COMO phasing