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Crystal structure of Sec4 in complex with 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 5.5 293 12% PEG MME 2000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.34 71.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.9 α = 90 b = 131.9 β = 90 c = 217.562 γ = 120
Symmetry Space Group P 32 2 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 0.9816 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 2.9 19.9 99.3 49236 48896 -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) 2.9 2.95 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 2.9 15 46245 46245 2437 99.72 0.2202 0.2202 0.21773 0.2201 0.26763 0.2655 RANDOM
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 36.029 r_dihedral_angle_4_deg 17.284 r_dihedral_angle_3_deg 16.469 r_dihedral_angle_1_deg 5.879 r_scangle_it 1.135 r_angle_refined_deg 1.12 r_angle_other_deg 0.824 r_scbond_it 0.714 r_mcangle_it 0.675 r_mcbond_it 0.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.029 r_dihedral_angle_4_deg 17.284 r_dihedral_angle_3_deg 16.469 r_dihedral_angle_1_deg 5.879 r_scangle_it 1.135 r_angle_refined_deg 1.12 r_angle_other_deg 0.824 r_scbond_it 0.714 r_mcangle_it 0.675 r_mcbond_it 0.616 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.186 r_nbd_other 0.179 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.161 r_symmetry_vdw_other 0.139 r_symmetry_vdw_refined 0.102 r_nbtor_other 0.082 r_chiral_restr 0.061 r_mcbond_other 0.05 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8373 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing