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Crystal structure of GTP-bound Rab11 in complex with FIP3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZK PDB Entry: 1YZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 20% PEG4000, 0.4M Ammonium Sulfate, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.291 α = 90 b = 52.601 β = 105.56 c = 70.679 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 IMAGE PLATE MAR scanner 300 mm plate 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.85 50 97.1 0.051 27.5 4 64429 64451
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) 1.85 1.9 77 0.259 5 4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry: 1YZK 1.86 8 60337 3221 98.24 0.2051 0.2034 0.2369 0.2559 RANDOM 29.957
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] -0.45 1.3 0.27 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.644 r_dihedral_angle_4_deg 16.837 r_dihedral_angle_3_deg 12.026 r_dihedral_angle_1_deg 4.846 r_scangle_it 1.545 r_scbond_it 0.973 r_angle_refined_deg 0.972 r_mcangle_it 0.692 r_mcbond_it 0.411 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.644 r_dihedral_angle_4_deg 16.837 r_dihedral_angle_3_deg 12.026 r_dihedral_angle_1_deg 4.846 r_scangle_it 1.545 r_scbond_it 0.973 r_angle_refined_deg 0.972 r_mcangle_it 0.692 r_mcbond_it 0.411 r_nbtor_refined 0.295 r_nbd_refined 0.176 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.124 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.062 r_metal_ion_refined 0.027 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5073 Nucleic Acid Atoms Solvent Atoms 906 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing