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Crystal structure of a xylose isomerase domain containing protein (stm4435) from salmonella typhimurium lt2 at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NANODROP, 20.0% Glycerol, 0.16M Mg(OAc)2, 16.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.5 α = 90 b = 95.23 β = 90 c = 136.71 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97922, 0.97894 SSRL BL11-1
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 2.4 29.386 98.5 0.057 9.83 48661 -3 44.32
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 2.4 2.49 92.4 0.322 2.4
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 MAD THROUGHOUT 2.4 29.386 48605 2435 99.3 0.186 0.184 0.191 0.228 0.2313 RANDOM 44.088
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] -1.36 -1.38 2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.112 r_dihedral_angle_4_deg 20.184 r_dihedral_angle_3_deg 14.895 r_dihedral_angle_1_deg 5.99 r_scangle_it 4.625 r_scbond_it 3.504 r_mcangle_it 1.533 r_angle_refined_deg 1.333 r_mcbond_it 1.114 r_angle_other_deg 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.112 r_dihedral_angle_4_deg 20.184 r_dihedral_angle_3_deg 14.895 r_dihedral_angle_1_deg 5.99 r_scangle_it 4.625 r_scbond_it 3.504 r_mcangle_it 1.533 r_angle_refined_deg 1.333 r_mcbond_it 1.114 r_angle_other_deg 0.82 r_mcbond_other 0.433 r_symmetry_vdw_other 0.228 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.182 r_nbd_other 0.18 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.104 r_nbtor_other 0.084 r_chiral_restr 0.071 r_metal_ion_refined 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8552 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing