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Structure of yiht from Salmonella typhimurium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 8% Glycerol; Cryoprotectant - 2% PEG 4000, 0.1M Cacodylate pH 6.5, 1.5M NaKPhosphate pH 8.5, 30% Glycerol, 1M NaBr, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.87 67.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.144 α = 90 b = 141.144 β = 90 c = 102.726 γ = 90
Symmetry Space Group I 41 2 2
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 MARRESEARCH Vertical and horizontal focusing mirrors 2003-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979 APS 31-ID
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 2.7 20 99.2 0.123 9.4 5.4 14427 14427 -3 61
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) 2.7 2.8 99.6 0.324 4.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.7 20 -3 14392 14392 721 99.23 0.18018 0.18018 0.17867 0.1833 0.20825 0.2166 RANDOM 40.502
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] -1.78 -1.78 3.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_3_deg 17.564 r_dihedral_angle_4_deg 16.662 r_dihedral_angle_1_deg 5.434 r_scangle_it 2.319 r_scbond_it 1.526 r_angle_refined_deg 1.467 r_mcangle_it 0.956 r_angle_other_deg 0.836 r_mcbond_it 0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.692 r_dihedral_angle_3_deg 17.564 r_dihedral_angle_4_deg 16.662 r_dihedral_angle_1_deg 5.434 r_scangle_it 2.319 r_scbond_it 1.526 r_angle_refined_deg 1.467 r_mcangle_it 0.956 r_angle_other_deg 0.836 r_mcbond_it 0.831 r_symmetry_vdw_other 0.268 r_nbd_refined 0.222 r_nbd_other 0.195 r_symmetry_hbond_refined 0.191 r_xyhbond_nbd_refined 0.185 r_symmetry_vdw_refined 0.185 r_mcbond_other 0.119 r_nbtor_other 0.091 r_chiral_restr 0.076 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2218 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing