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Crystal structure of the Propionibacterium acnes surface sialidase in complex with Neu5Ac2en
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 6.8 291 18% (w/v) polyethylene glycol monomethylether 2000, 100 mM HEPES, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.01 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.978 α = 116.93 b = 46.65 β = 99.1 c = 49.659 γ = 91.73
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 1.7 50 93.2 0.04 20.17 3.9 33635
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 1.7 1.76 88.2 0.24 4.43 3.5
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 1.7 43.44 33635 1796 92.79 0.1532 0.1517 0.1574 0.1816 0.1883 RANDOM 29.48
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] -0.49 0.29 0.05 1.07 0.56 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.071 r_dihedral_angle_4_deg 16.127 r_dihedral_angle_3_deg 11.421 r_dihedral_angle_1_deg 7.483 r_angle_refined_deg 2.047 r_chiral_restr 0.154 r_bond_refined_d 0.021 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 25
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing