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Structure of GTP-Bound Rab4Q67L GTPase in complex with the central Rab binding domain of Rabenosyn-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Rab4 GTPase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 20% PEG 4000, 200mM ammonium fluoride, 50mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.58 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.44 α = 90 b = 81.44 β = 90 c = 137.639 γ = 120
Symmetry Space Group P 31 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 osmic mirror 2004-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.9 50 99.6 0.054 27.29 5 42193 41.7
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) 1.9 1.96 98.9 0.379 4 5 3439
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 Rab4 GTPase 1.92 15 42214 38744 2072 99.68 0.24 0.22538 0.22356 0.2242 0.25889 0.2623 RANDOM 33.045
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] 1.2 0.6 1.2 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.918 r_dihedral_angle_4_deg 19.757 r_dihedral_angle_3_deg 12.886 r_dihedral_angle_1_deg 5.341 r_scangle_it 1.953 r_angle_refined_deg 1.302 r_scbond_it 1.243 r_mcangle_it 1.053 r_mcbond_it 0.626 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.918 r_dihedral_angle_4_deg 19.757 r_dihedral_angle_3_deg 12.886 r_dihedral_angle_1_deg 5.341 r_scangle_it 1.953 r_angle_refined_deg 1.302 r_scbond_it 1.243 r_mcangle_it 1.053 r_mcbond_it 0.626 r_nbtor_refined 0.297 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.126 r_chiral_restr 0.114 r_bond_refined_d 0.008 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_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 3573 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing