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Structural basis for high arginine specificity in Salmonella typhimurium periplasmic binding protein STM4351.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LAH PDB ENTRY 1LAH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 18% PEG 8000, 100MM SODIUM CACODYLATE, 200MM ZINC ACETATE., pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.3 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.317 α = 90 b = 56.331 β = 100.17 c = 88.37 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 273 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.9 47.28 99.8 0.1 17.9 6 35156 2.4 21.7
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 1.88 1.95 99.1 0.86 2.4 5.2
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 PDB ENTRY 1LAH 1.9 47.28 35156 1856 99.87 0.19949 0.19805 0.1988 0.22602 0.2262 RANDOM 27.965
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] 1.17 -0.04 -0.12 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.454 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 5.645 r_scangle_it 2.194 r_scbond_it 1.338 r_angle_refined_deg 1.084 r_mcangle_it 0.795 r_mcbond_it 0.414 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.454 r_dihedral_angle_4_deg 18.907 r_dihedral_angle_3_deg 14.157 r_dihedral_angle_1_deg 5.645 r_scangle_it 2.194 r_scbond_it 1.338 r_angle_refined_deg 1.084 r_mcangle_it 0.795 r_mcbond_it 0.414 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3558 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing