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Crystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) R77A mutant from Salmonella typhimurium complexed with histidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LAG
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 2.43 49.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.199 α = 90 b = 58.85 β = 90 c = 115.282 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 PIXEL DECTRIS PILATUS 200K Osmic VariMax Cu-HF 2018-05-18 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) 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 1.88 50 99.4 0.106 26.9 6.5 40663 21.4
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 1.88 1.91 94.9 0.63 0.667 2.3 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1LAG 1.883 41.179 1.34 38630 1971 97.65 0.1683 0.1636 0.166 0.2134 0.2127
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.433 f_angle_d 0.983 f_chiral_restr 0.04 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1809 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing