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Crystal structure of yeast Rab-GDI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKV PDB ENTRY 1ukv, chain G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.39 63.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.46 α = 90 b = 159.78 β = 90.25 c = 77.093 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 CCD MARMOSAIC 325 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9795 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 19.97 98.5 60538 59630 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.35 80
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1ukv, chain G 2.3 19.97 60538 56646 2982 100 0.2 0.1992 0.19688 0.1942 0.2426 0.239 RANDOM 38.073
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] -0.48 -0.07 -0.41 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_4_deg 15.921 r_dihedral_angle_3_deg 15.863 r_dihedral_angle_1_deg 5.419 r_scangle_it 1.866 r_scbond_it 1.136 r_angle_refined_deg 1.058 r_mcangle_it 0.954 r_mcbond_it 0.533 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.562 r_dihedral_angle_4_deg 15.921 r_dihedral_angle_3_deg 15.863 r_dihedral_angle_1_deg 5.419 r_scangle_it 1.866 r_scbond_it 1.136 r_angle_refined_deg 1.058 r_mcangle_it 0.954 r_mcbond_it 0.533 r_nbtor_refined 0.302 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.143 r_xyhbond_nbd_refined 0.134 r_symmetry_vdw_refined 0.113 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6979 Nucleic Acid Atoms Solvent Atoms 797 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XDS data scaling MOLREP phasing