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Structural Basis for the Selectivity of Guanine Nucleotide Exchange Factors for the small G-protein Ral
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JGW 4JGW as poly Ala model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.45 289 15% PEG 3350, 200 mM ammonium acetate, 100 mM Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.877 α = 90 b = 99.828 β = 127 c = 111.487 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 315r 2012-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97488 ESRF ID23-1
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 2.6 50 88.5 0.127 12.72 2.8 40751
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.7 56.8 2.69 1.8
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 4JGW as poly Ala model 2.6 46.63 38712 2038 100 0.27573 0.27332 0.2686 0.31988 0.3158 RANDOM 58.171
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] 0.63 -0.46 1.03 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 18.634 r_dihedral_angle_3_deg 16.876 r_dihedral_angle_1_deg 4.373 r_scangle_it 1.256 r_angle_refined_deg 0.925 r_scbond_it 0.726 r_mcangle_it 0.634 r_mcbond_it 0.327 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.82 r_dihedral_angle_4_deg 18.634 r_dihedral_angle_3_deg 16.876 r_dihedral_angle_1_deg 4.373 r_scangle_it 1.256 r_angle_refined_deg 0.925 r_scbond_it 0.726 r_mcangle_it 0.634 r_mcbond_it 0.327 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 8583 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing