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Crystal structure of solute-binding protein stm0429 from salmonella enterica subsp. enterica serovar typhimurium str. lt2, target efi-510776, a closed conformation, in complex with glycerol and acetate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100); RESERVOIR: 0.17 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE:HCL, PH 5.6, 25% PEG4000, 15% GLYCEROL; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.185 α = 90 b = 67.601 β = 90 c = 77.36 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 2014-07-18 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 1.22 50 98 0.062 0.062 25.9 6.7 85094 -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 1.22 1.24 77.4 0.5 0.5 2.1 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.22 50 82436 2576 97.81 0.11469 0.11367 0.133 0.14781 0.1649 RANDOM 21.284
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] -0.74 1.14 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.132 r_sphericity_free 32.491 r_dihedral_angle_4_deg 22.812 r_sphericity_bonded 12.643 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_1_deg 6.456 r_long_range_B_refined 5.69 r_scbond_it 5.375 r_scbond_other 5.372 r_rigid_bond_restr 5.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.132 r_sphericity_free 32.491 r_dihedral_angle_4_deg 22.812 r_sphericity_bonded 12.643 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_1_deg 6.456 r_long_range_B_refined 5.69 r_scbond_it 5.375 r_scbond_other 5.372 r_rigid_bond_restr 5.287 r_long_range_B_other 5.213 r_scangle_other 4.801 r_mcangle_other 3.587 r_mcangle_it 3.585 r_mcbond_it 3.054 r_mcbond_other 3.043 r_angle_refined_deg 1.914 r_angle_other_deg 1.347 r_chiral_restr 0.132 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.007 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2430 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 10
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing