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Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with Siastatin B
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 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.1 M CAPS pH 10.5
Crystal Properties Matthews coefficient Solvent content 2.32 46.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.109 α = 90 b = 99.109 β = 90 c = 131.708 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 2014-09-25 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 1.94 50 98.3 0.066 14.5 3.1 34757
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 1.94 1.97 97.7 0.458 3 1678
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2sli 1.94 71.91 1586 97.5 0.1793 0.177 0.225 0.2141 RANDOM 27.04
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] 0.54 0.27 0.54 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.068 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_4_deg 12.547 r_dihedral_angle_1_deg 7.491 r_mcangle_it 2.879 r_mcbond_it 2.234 r_mcbond_other 2.234 r_angle_refined_deg 1.898 r_angle_other_deg 0.87 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.068 r_dihedral_angle_3_deg 13.524 r_dihedral_angle_4_deg 12.547 r_dihedral_angle_1_deg 7.491 r_mcangle_it 2.879 r_mcbond_it 2.234 r_mcbond_other 2.234 r_angle_refined_deg 1.898 r_angle_other_deg 0.87 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3778 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building HKL-2000 data reduction