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Structural Basis of Promiscuous Guanine Nucleotide Exchange by the T-Cell Essential Vav1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 17% PEG-3350, 100 mM HEPES, pH 7.5, 200 mM ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.948 α = 90 b = 75.079 β = 103.87 c = 114.857 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 300 mm CCD mirrors 2006-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.95 APS 23-ID-B
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 2.6 30 100 3 36259 36156
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.667 100 1861
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 SAD THROUGHOUT 1FOE 2.6 30 1 1 38095 36156 1939 100 0.22473 0.2211 0.2298 0.29253 0.3026 RANDOM 36.506
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] -0.12 -0.1 0.06 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.972 r_dihedral_angle_3_deg 21.201 r_dihedral_angle_4_deg 20.349 r_dihedral_angle_1_deg 14.024 r_scangle_it 2.305 r_angle_refined_deg 1.825 r_angle_other_deg 1.448 r_scbond_it 1.428 r_mcangle_it 1.19 r_mcbond_it 0.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.972 r_dihedral_angle_3_deg 21.201 r_dihedral_angle_4_deg 20.349 r_dihedral_angle_1_deg 14.024 r_scangle_it 2.305 r_angle_refined_deg 1.825 r_angle_other_deg 1.448 r_scbond_it 1.428 r_mcangle_it 1.19 r_mcbond_it 0.691 r_symmetry_hbond_refined 0.35 r_chiral_restr 0.276 r_nbd_refined 0.243 r_symmetry_vdw_other 0.227 r_nbd_other 0.212 r_symmetry_vdw_refined 0.205 r_nbtor_refined 0.194 r_xyhbond_nbd_refined 0.18 r_metal_ion_refined 0.169 r_nbtor_other 0.097 r_mcbond_other 0.094 r_xyhbond_nbd_other 0.059 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8359 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing