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Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from Legionella pneumophila
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.75 292 0.1 M Sodium citrate, 35% v/v PEG 600, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.756 α = 90 b = 100.756 β = 90 c = 146.36 γ = 120
Symmetry Space Group P 63 2 2
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 MARMOSAIC 225 mm CCD 2008-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000000 SLS X10SA
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 1.8 30 98.1 0.09 21.97 40529 -3 33.85
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 1.8 1.9 97.1 0.456 4.7
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 SAD THROUGHOUT 1.8 29.63 40517 2005 98.13 0.202 0.201 0.2262 0.234 0.2563 RANDOM 17.349
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] -2.79 -1.4 -2.79 4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.354 r_dihedral_angle_4_deg 15.583 r_dihedral_angle_3_deg 14.364 r_dihedral_angle_1_deg 6.405 r_scangle_it 4.731 r_scbond_it 3.123 r_mcangle_it 2.067 r_angle_refined_deg 1.829 r_mcbond_it 1.292 r_angle_other_deg 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.354 r_dihedral_angle_4_deg 15.583 r_dihedral_angle_3_deg 14.364 r_dihedral_angle_1_deg 6.405 r_scangle_it 4.731 r_scbond_it 3.123 r_mcangle_it 2.067 r_angle_refined_deg 1.829 r_mcbond_it 1.292 r_angle_other_deg 1.05 r_mcbond_other 0.464 r_chiral_restr 0.123 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2818 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 5
Software Software Software Name Purpose XSCALE data scaling SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction