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Crystal structure of the Propionibacterium acnes surface sialidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291 20% (w/v) polyethylene glycol monomethylether 2000, 100 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.973 α = 116.51 b = 46.847 β = 98.94 c = 49.6 γ = 91.69
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 50 91.8 0.05 18.26 3.9 17676 29.05
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 2.1 2.18 77.4 0.235 3.6
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 1EUR 2.11 43.6 17676 967 92.98 0.1759 0.1726 0.1751 0.2328 0.2357 RANDOM 39.361
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] -0.12 0.34 0.22 0.37 -0.07 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.505 r_dihedral_angle_4_deg 16.739 r_dihedral_angle_3_deg 14.68 r_dihedral_angle_1_deg 7.497 r_angle_refined_deg 1.913 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 9
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing