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Crystal structure of D. melanogaster Rab6 GTPase bound to GMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YZQ PDB ENTRY 1YZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 2.4 M AMMONIUM SULPHATE, 0.1 M IMIDAZOLE PH 8.0, 2.5% PEG 400, 2.5% DMSO AND 3% TRIMETHYLAMINE N-OXIDE.
Crystal Properties Matthews coefficient Solvent content 1.92 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.52 α = 90 b = 42.71 β = 133.12 c = 86.86 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 CCD ADSC CCD 2010-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.39 31.7 97.4 0.05 9.7 3.5 61395 12.326
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.47 95.3 0.28 4.4 3.4
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 1YZQ 1.39 63.4 58225 3121 97.32 0.14607 0.14458 0.17296 0.1905 RANDOM 11.573
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] 0.26 -0.29 -0.15 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_4_deg 17.056 r_dihedral_angle_3_deg 12.006 r_dihedral_angle_1_deg 5.947 r_scangle_it 5.236 r_scbond_it 3.503 r_mcangle_it 2.44 r_angle_refined_deg 1.561 r_mcbond_it 1.478 r_rigid_bond_restr 1.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_4_deg 17.056 r_dihedral_angle_3_deg 12.006 r_dihedral_angle_1_deg 5.947 r_scangle_it 5.236 r_scbond_it 3.503 r_mcangle_it 2.44 r_angle_refined_deg 1.561 r_mcbond_it 1.478 r_rigid_bond_restr 1.346 r_angle_other_deg 0.928 r_mcbond_other 0.417 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2682 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing