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2.6 Angstrom Structure of the Extracellular Solute-binding Protein from Staphylococcus aureus in complex with PEG.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZYO PDB ENTRY 2ZYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.4mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3;
Screen: JCSG+ (B12), 0.2M tri-Potassium citrate pH 8.3, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3 58.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.863 α = 90 b = 101.863 β = 90 c = 191.341 γ = 120
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 2012-10-18 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 2.6 30 98.8 0.09 17.7 5.4 34117 34117 -3 57.5
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 2.6 2.64 99.6 0.644 3 5.4 1701
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 PDB ENTRY 2ZYO 2.6 29.99 32393 32393 1721 98.99 0.17003 0.17003 0.16742 0.1678 0.21933 0.2098 RANDOM 39.585
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] 3.05 1.52 3.05 -4.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_3_deg 11.515 r_dihedral_angle_4_deg 10.949 r_scangle_it 5.358 r_scbond_it 3.393 r_dihedral_angle_1_deg 2.885 r_mcangle_it 1.979 r_angle_refined_deg 1.37 r_mcbond_it 1.044 r_angle_other_deg 0.805
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_3_deg 11.515 r_dihedral_angle_4_deg 10.949 r_scangle_it 5.358 r_scbond_it 3.393 r_dihedral_angle_1_deg 2.885 r_mcangle_it 1.979 r_angle_refined_deg 1.37 r_mcbond_it 1.044 r_angle_other_deg 0.805 r_mcbond_other 0.246 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6032 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 60
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling