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Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J5X PDB ENTRY 2J5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.0 M AMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.2 M NACL, 2 MM MGCL2, 6 % MPD
Crystal Properties Matthews coefficient Solvent content 2.99 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.27 α = 90 b = 137.27 β = 90 c = 165.03 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 IMAGE PLATE MAR555 FLAT PANEL 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.93 35 99.9 0.06 8 12.8 62165 2
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 1.93 2.03 98.2 0.4 2.1 11.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2J5X 1.93 118.68 62165 6987 99.9 0.217 0.214 0.2096 0.238 0.2317 RANDOM 30.43
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] 1.03 0.52 1.03 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.731 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_1_deg 5.367 r_scangle_it 2.462 r_scbond_it 1.541 r_angle_refined_deg 1.17 r_mcangle_it 1.104 r_mcbond_it 0.686 r_symmetry_hbond_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.731 r_dihedral_angle_3_deg 15.539 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_1_deg 5.367 r_scangle_it 2.462 r_scbond_it 1.541 r_angle_refined_deg 1.17 r_mcangle_it 1.104 r_mcbond_it 0.686 r_symmetry_hbond_refined 0.335 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4931 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing