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Crystal Structure of Rab5b GTPase domain from Leishmania donovani in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Sodium Acetate,
MES Hydrate pH 6.7,
PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.066 α = 90 b = 61.861 β = 90 c = 73.635 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS EIGER2 X CdTe 16M 2023-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.885 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.5 47.4 99.9 0.996 8.3 6.2 6617
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.964
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 (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 2.5 47.36 5947 620 99.88 0.22038 0.21575 0.2192 0.26324 0.2626 RANDOM 49.442
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] 10.8 -5.89 -4.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.155 r_long_range_B_refined 14.405 r_long_range_B_other 14.376 r_dihedral_angle_2_deg 12.857 r_mcangle_it 8.154 r_mcangle_other 8.151 r_scangle_other 7.6 r_dihedral_angle_1_deg 6.605 r_mcbond_it 5.09 r_mcbond_other 5.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.155 r_long_range_B_refined 14.405 r_long_range_B_other 14.376 r_dihedral_angle_2_deg 12.857 r_mcangle_it 8.154 r_mcangle_other 8.151 r_scangle_other 7.6 r_dihedral_angle_1_deg 6.605 r_mcbond_it 5.09 r_mcbond_other 5.088 r_scbond_it 4.758 r_scbond_other 4.756 r_rigid_bond_restr 1.933 r_angle_refined_deg 1.409 r_angle_other_deg 0.871 r_chiral_restr 0.093 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d 0.006 r_gen_planes_other 0.006 r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1133 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing