☰ Navigation Tabs
Functional annotation of Salmonella enterica yihS-encoded protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 15% PEG10000, 0.1M Tris-HCl, pH8.0, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.229 α = 106.86 b = 89.807 β = 104.43 c = 94.73 γ = 110.31
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 RIGAKU JUPITER 210 2007-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.6 50 94.1 0.062 10.6 2.8 297314 12.4
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) 1.6 1.66 86.4 0.376 1.3 2.5 27327
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 2AFA 1.6 15 282225 14777 93.8 0.15363 0.15217 0.1533 0.18158 0.1533 RANDOM 13.087
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] -0.11 0.29 -0.33 0.19 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.16 r_dihedral_angle_4_deg 17.158 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 5.376 r_scangle_it 2.626 r_scbond_it 1.75 r_angle_refined_deg 1.213 r_mcangle_it 1.015 r_mcbond_it 0.652 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.16 r_dihedral_angle_4_deg 17.158 r_dihedral_angle_3_deg 13.019 r_dihedral_angle_1_deg 5.376 r_scangle_it 2.626 r_scbond_it 1.75 r_angle_refined_deg 1.213 r_mcangle_it 1.015 r_mcbond_it 0.652 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.251 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20639 Nucleic Acid Atoms Solvent Atoms 2941 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing