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Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with 2,7-Anhydro-Neu5Ac
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 micro seeding into 0.8 M NaH2PO4, 1.2M K2HPO4, sodium acetate 0.1M pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.257 α = 90 b = 99.257 β = 90 c = 130.599 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 RIGAKU SATURN 944 2014-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.71 45 92.9 0.049 20 4.2 48126
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 1.71 1.74 53 0.421 2.4 1358
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.71 45 45702 2250 92.54 0.1454 0.1432 0.1553 0.1884 0.1986 RANDOM 29.958
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] 0.73 0.36 0.73 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.169 r_dihedral_angle_4_deg 18.251 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 7.781 r_mcangle_it 3.238 r_mcbond_it 2.516 r_mcbond_other 2.515 r_angle_refined_deg 1.891 r_angle_other_deg 0.883 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.169 r_dihedral_angle_4_deg 18.251 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 7.781 r_mcangle_it 3.238 r_mcbond_it 2.516 r_mcbond_other 2.515 r_angle_refined_deg 1.891 r_angle_other_deg 0.883 r_chiral_restr 0.122 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3779 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 46
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building