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1.0 Angstrom resolution crystal structure of the branched-chain amino acid transporter substrate binding protein LivJ from Streptococcus pneumoniae str. Canada MDR_19A in complex with Isoleucine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 Protein at 66 mg/mL, Crystallization condition: PEG 4K 30% w/v Mg Chloride 0.2M Tris0.1M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.274 α = 90 b = 72.819 β = 105.1 c = 57.542 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 Be-Lenses 2012-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 30 99.7 0.048 22.85 4.5 159549 159549 -3 7
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 1.02 98 0.487 2.2 3 7818
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 1z18 1 27.78 151086 151086 7976 99.69 0.12722 0.12622 0.1263 0.14656 0.1453 RANDOM 9.151
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] 0.07 -0.1 0.09 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_3_deg 8.186 r_dihedral_angle_4_deg 6.454 r_scangle_it 4.383 r_dihedral_angle_1_deg 3.47 r_scbond_it 2.917 r_mcbond_other 2.572 r_mcangle_it 2.105 r_angle_refined_deg 1.747 r_mcbond_it 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_3_deg 8.186 r_dihedral_angle_4_deg 6.454 r_scangle_it 4.383 r_dihedral_angle_1_deg 3.47 r_scbond_it 2.917 r_mcbond_other 2.572 r_mcangle_it 2.105 r_angle_refined_deg 1.747 r_mcbond_it 1.41 r_rigid_bond_restr 1.317 r_angle_other_deg 1.084 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2582 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 14
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling