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Crystal Structure of Gyp1 TBC domain in complex with Rab33 GTPase bound to GDP and AlF3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 277 10~15% polyethylene glycol 6000, 100 mM Sodium Acetate, 10% Glycerol, 20 mM NaF, 2mM AlCl3, 50 mM HEPES, pH7.0, EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.2 α = 90 b = 94.526 β = 90 c = 102.561 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 4 2005-02-09 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2005-02-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979026 NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X29A 0.9793, 0.9790, 0.9670 NSLS X29A
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 1,2 2.26 50 99 0.065 9.9 5 62674 33046 37.6 1017 27
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) 2.26 2.34 99.9 0.354 4.93 5.1 6309
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.26 8 30553 1634 98.65 0.207 0.20726 0.20524 0.1814 0.24357 RANDOM 39.538
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] -1.88 4.63 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.869 r_dihedral_angle_4_deg 14.393 r_dihedral_angle_3_deg 14.166 r_dihedral_angle_1_deg 4.713 r_scangle_it 1.32 r_angle_refined_deg 0.987 r_mcangle_it 0.912 r_scbond_it 0.817 r_mcbond_it 0.519 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.869 r_dihedral_angle_4_deg 14.393 r_dihedral_angle_3_deg 14.166 r_dihedral_angle_1_deg 4.713 r_scangle_it 1.32 r_angle_refined_deg 0.987 r_mcangle_it 0.912 r_scbond_it 0.817 r_mcbond_it 0.519 r_nbtor_refined 0.298 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.166 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_refined 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 4141 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SHARP phasing