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Ruminococcus gnavus IT-sialidase CBM40 bound to alpha2,3 sialyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium chloride with 20% PEG 8000
crystal growth time was improved using micro-seeding
Crystals were cryoprotected using the crystallisation condition supplemented with 25% (w/w) glycerol
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.8 α = 90 b = 72.35 β = 105.1 c = 51.52 γ = 90
Symmetry Space Group P 1 21 1
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+ 2015-08-13 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) Rrim I (All) 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 1.37 49.91 74.3 0.036 0.04 22.94 4.3 53954 -3 19.974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.41 11.1 0.344 0.437 2.99 2.4
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 2VW2 1.37 39.48 51221 2709 74.33 0.1512 0.1493 0.1494 0.1872 0.1872 RANDOM 17.572
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] 0.48 -0.55 -0.12 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.361 r_dihedral_angle_4_deg 16.573 r_dihedral_angle_3_deg 12.797 r_dihedral_angle_1_deg 6.763 r_mcbond_other 5.477 r_mcbond_it 5.476 r_mcangle_it 5.311 r_angle_refined_deg 1.649 r_angle_other_deg 1.118 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.361 r_dihedral_angle_4_deg 16.573 r_dihedral_angle_3_deg 12.797 r_dihedral_angle_1_deg 6.763 r_mcbond_other 5.477 r_mcbond_it 5.476 r_mcangle_it 5.311 r_angle_refined_deg 1.649 r_angle_other_deg 1.118 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2781 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 70
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction