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Crystal structure of Ypt31 in complex with 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 2.41 48.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.94 α = 90 b = 61.43 β = 103.68 c = 92.75 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 0.931 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 2.35 19.79 99.7 30772 30683 -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) 2.35 2.4 99.7
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 2.35 19.79 28714 28714 1512 100 0.20156 0.20156 0.19875 0.2004 0.25523 0.2537 RANDOM 42.168
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.739 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_1_deg 5.414 r_scangle_it 1.791 r_angle_refined_deg 1.102 r_scbond_it 1.079 r_mcangle_it 0.832 r_mcbond_it 0.472 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.739 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_3_deg 15.041 r_dihedral_angle_1_deg 5.414 r_scangle_it 1.791 r_angle_refined_deg 1.102 r_scbond_it 1.079 r_mcangle_it 0.832 r_mcbond_it 0.472 r_nbtor_refined 0.298 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.172 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.071 r_metal_ion_refined 0.029 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4749 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing