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2.1 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5). Screen solution: 0.2M Sodium acetate, 0.1M Bis-Tris (pH 6.5), 0.01M Glycolic acid, 30% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.495 α = 90 b = 139.371 β = 90 c = 111.043 γ = 90
Symmetry Space Group C 2 2 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 225 mm CCD Beryllium lenses 2010-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.1 30 99.9 0.074 39.3 6.1 18836 18836 -3 36
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) 2.1 2.14 100 0.486 3.8 6.2 924
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 3KBO 2.1 29.51 17835 17835 967 99.84 0.19865 0.19865 0.19659 0.2042 0.23508 0.236 RANDOM 44.491
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] -0.95 -0.72 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.6 r_dihedral_angle_4_deg 14.205 r_dihedral_angle_3_deg 13.422 r_scangle_it 4.972 r_scbond_it 3.565 r_dihedral_angle_1_deg 3.508 r_mcangle_it 2.144 r_angle_refined_deg 1.396 r_mcbond_it 1.314 r_angle_other_deg 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.6 r_dihedral_angle_4_deg 14.205 r_dihedral_angle_3_deg 13.422 r_scangle_it 4.972 r_scbond_it 3.565 r_dihedral_angle_1_deg 3.508 r_mcangle_it 2.144 r_angle_refined_deg 1.396 r_mcbond_it 1.314 r_angle_other_deg 0.816 r_mcbond_other 0.41 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2449 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing