☰ Navigation Tabs
Crystal structure of GppNHp bound GTPase domain of Rab5a from Leishmania donovani
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N6H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.2M Magnesium Acetate, 0.1M Tris-HCl pH 8.5, 19% PEG 8K
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.552 α = 90 b = 42.266 β = 103.387 c = 37.777 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 RIGAKU RAXIS IV++ 2023-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.798 35 99.7 0.054 25 6.6 15882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 97.7 0.22 0.242 0.1 0.975 5.6
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.798 27.354 15882 793 99.449 0.164 0.1616 0.1617 0.2029 0.2028 26.533
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] 0.04 0.248 0.152 -0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.582 r_dihedral_angle_4_deg 17.837 r_dihedral_angle_3_deg 14.703 r_lrange_it 7.142 r_dihedral_angle_1_deg 6.267 r_scangle_it 5.104 r_mcangle_it 3.901 r_scbond_it 3.385 r_mcbond_it 2.553 r_angle_refined_deg 2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.582 r_dihedral_angle_4_deg 17.837 r_dihedral_angle_3_deg 14.703 r_lrange_it 7.142 r_dihedral_angle_1_deg 6.267 r_scangle_it 5.104 r_mcangle_it 3.901 r_scbond_it 3.385 r_mcbond_it 2.553 r_angle_refined_deg 2.13 r_nbtor_refined 0.317 r_nbd_refined 0.239 r_symmetry_nbd_refined 0.18 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.157 r_chiral_restr 0.153 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_metal_ion_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1235 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing