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ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R8R PDB ENTRY 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 1.88M Ammonium Sulfate, 100mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.018 α = 90 b = 104.018 β = 90 c = 69.277 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.46 30 0.059 26.6 16 75051 18.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.47 97 0.462 5.9 12.1
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 (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 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48) 1.46 28.87 75051 71299 3744 99.91 0.15941 0.15885 0.1585 0.1698 0.1718 RANDOM 12.525
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] -0.05 -0.02 -0.05 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.153 r_scangle_it 4.08 r_scbond_it 2.529 r_mcangle_it 1.68 r_angle_refined_deg 1.421 r_mcbond_it 0.881 r_angle_other_deg 0.87 r_symmetry_vdw_refined 0.56 r_symmetry_vdw_other 0.31 r_nbd_other 0.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.153 r_scangle_it 4.08 r_scbond_it 2.529 r_mcangle_it 1.68 r_angle_refined_deg 1.421 r_mcbond_it 0.881 r_angle_other_deg 0.87 r_symmetry_vdw_refined 0.56 r_symmetry_vdw_other 0.31 r_nbd_other 0.246 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.086 r_nbtor_other 0.085 r_gen_planes_other 0.022 r_bond_other_d 0.018 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling CCP4 phasing