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Structure of GTP-Bound Rab22Q64L GTPase in complex with the minimal Rab binding domain of Rabenosyn-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Rab22 GTPase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 10% PEG 6000, 50mM Na acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.075 α = 90 b = 55.897 β = 90 c = 85.96 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 315 2004-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10 NSLS X25
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 1.3 50 85.2 0.038 54.1 10 46168 21.5
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 1.3 1.34 49.9 0.381 3.8 10 2217
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-Factor (All) 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 Rab22 GTPase 1.32 15 46206 42797 2264 87.07 0.206 0.21536 0.21436 0.2094 0.23481 0.2321 RANDOM 19.034
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] -0.2 0.3 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.389 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_4_deg 12.094 r_dihedral_angle_1_deg 5.414 r_angle_refined_deg 1.19 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.389 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_4_deg 12.094 r_dihedral_angle_1_deg 5.414 r_angle_refined_deg 1.19 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.194 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1716 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing