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Crystal structure of ABC transporter substrate-binding protein YesO from Bacillus subtilis, TARGET EFI-510761, an open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 Protein: 10 mM BIS-TRIS, 500 mm NaCl, 5% glycerol, 5 mm DTT; reservoir: 1.4 m sodium citrate, 0.1 m HEPES-NaOH, pH 7.5; vapor diffusion, sitting drop, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.09 41.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.932 α = 90 b = 75.727 β = 90 c = 119.738 γ = 90
Symmetry Space Group P 21 21 21
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 315 MIRRORS 2014-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.94 50 99.3 0.079 0.079 25 6.9 30836 -5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.97 94.2 0.78 0.78 1.7 5.7
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 MR THROUGHOUT 2DVU 1.94 50 29819 952 99.11 0.19383 0.1918 0.2008 0.25981 0.266 RANDOM 39.652
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] 2.17 -2.18 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.849 r_dihedral_angle_4_deg 20.309 r_dihedral_angle_3_deg 15.893 r_scangle_other 13.727 r_long_range_B_other 13.719 r_long_range_B_refined 13.656 r_scbond_it 13.434 r_scbond_other 13.434 r_mcangle_other 7.64 r_mcangle_it 7.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.849 r_dihedral_angle_4_deg 20.309 r_dihedral_angle_3_deg 15.893 r_scangle_other 13.727 r_long_range_B_other 13.719 r_long_range_B_refined 13.656 r_scbond_it 13.434 r_scbond_other 13.434 r_mcangle_other 7.64 r_mcangle_it 7.638 r_mcbond_it 7.528 r_mcbond_other 7.517 r_dihedral_angle_1_deg 5.524 r_angle_refined_deg 1.376 r_angle_other_deg 0.791 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3179 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 1
Software Software Software Name Purpose PHASER phasing ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling