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Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Neu5Ac2en
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 microseeding into 0.8 M NaH2PO4, 1.2M K2HPO4, sodium acetate 0.1M pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.305 α = 90 b = 101.305 β = 90 c = 131.939 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 2014-08-14 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 2 45 99.5 0.064 15.3 2.9 33968
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 2.03 99.7 0.49 2.6 1743
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 2sli 2 45 32166 1586 98.82 0.2174 0.2146 0.2221 0.2728 0.2784 RANDOM 40.44
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] 1.11 0.56 1.11 -3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.393 r_dihedral_angle_3_deg 16.035 r_dihedral_angle_4_deg 12.596 r_dihedral_angle_1_deg 7.526 r_mcangle_it 4.544 r_mcbond_it 3.481 r_mcbond_other 3.481 r_angle_refined_deg 1.787 r_angle_other_deg 0.829 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.393 r_dihedral_angle_3_deg 16.035 r_dihedral_angle_4_deg 12.596 r_dihedral_angle_1_deg 7.526 r_mcangle_it 4.544 r_mcbond_it 3.481 r_mcbond_other 3.481 r_angle_refined_deg 1.787 r_angle_other_deg 0.829 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3803 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 25
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building