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Crystal structure of Rab1b covalently modified with AMP at Y77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 298 15% (v/v) isopropanol, 15% (w/v) PEG4000, 0.1 M imidazole, 10 mM BaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.97 α = 90 b = 100.589 β = 102.43 c = 45.071 γ = 90
Symmetry Space Group P 1 21 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 PIXEL PILATUS 6M SI(111) 2010-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 1.7 19.8 99.8 0.053 15.8 33392 -3
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) 1.7 1.8 100 0.313 4.5
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 THROUGHOUT 1.7 19.8 31709 1658 99.84 0.1515 0.14958 0.1778 0.18686 0.2066 RANDOM 31.283
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] 0.47 -1.45 -1.4 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.981 r_dihedral_angle_4_deg 15.547 r_dihedral_angle_3_deg 14.405 r_dihedral_angle_1_deg 6.064 r_scangle_it 5.726 r_scbond_it 3.62 r_mcangle_it 2.421 r_angle_refined_deg 2.053 r_mcbond_it 1.395 r_angle_other_deg 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.981 r_dihedral_angle_4_deg 15.547 r_dihedral_angle_3_deg 14.405 r_dihedral_angle_1_deg 6.064 r_scangle_it 5.726 r_scbond_it 3.62 r_mcangle_it 2.421 r_angle_refined_deg 2.053 r_mcbond_it 1.395 r_angle_other_deg 1.06 r_mcbond_other 0.475 r_chiral_restr 0.129 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2701 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 112
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction