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Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) S70A mutant from Salmonella typhimurium complexed with arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291.15 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.06 40.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.087 α = 90 b = 37.241 β = 90.01 c = 102.036 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 PIXEL DECTRIS PILATUS 200K Osmic VariMax Cu-HF 2018-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.6 38.34 99.1 0.101 0.991 18.3 4.6 58580 13.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 99 0.259 0.939 6.8 2.8
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 1LAF 1.6 38.34 57275 1002 99.13 0.1923 0.19174 0.2058 0.2236 0.2399 RANDOM 16.643
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] 4.5 5.79 -6.58 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 16.717 r_dihedral_angle_3_deg 15.182 r_dihedral_angle_1_deg 7.285 r_long_range_B_refined 4.611 r_long_range_B_other 4.531 r_scangle_other 3.007 r_mcangle_it 2.546 r_mcangle_other 2.546 r_scbond_it 2.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 16.717 r_dihedral_angle_3_deg 15.182 r_dihedral_angle_1_deg 7.285 r_long_range_B_refined 4.611 r_long_range_B_other 4.531 r_scangle_other 3.007 r_mcangle_it 2.546 r_mcangle_other 2.546 r_scbond_it 2.012 r_scbond_other 2.012 r_angle_refined_deg 1.909 r_mcbond_it 1.734 r_mcbond_other 1.733 r_angle_other_deg 1.417 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 3621 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing