☰ Navigation Tabs
Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in complex with oseltamivir carboxylate
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 micro seeding into 12.5% PEG 3350, 200 mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.4 48.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.097 α = 90 b = 101.097 β = 90 c = 131.537 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 2014-10-10 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 2.01 100 98.3 0.068 14.2 2.7 32612
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 2.01 2.04 97.2 0.499 2.4 1583
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 2.01 72.88 32166 1507 97.46 0.1871 0.1841 0.1927 0.2452 0.2519 RANDOM 30.888
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] 0.65 0.32 0.65 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 17.152 r_dihedral_angle_3_deg 14.66 r_dihedral_angle_1_deg 7.476 r_mcangle_it 3.31 r_mcbond_it 2.411 r_mcbond_other 2.411 r_angle_refined_deg 1.802 r_angle_other_deg 0.827 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 17.152 r_dihedral_angle_3_deg 14.66 r_dihedral_angle_1_deg 7.476 r_mcangle_it 3.31 r_mcbond_it 2.411 r_mcbond_other 2.411 r_angle_refined_deg 1.802 r_angle_other_deg 0.827 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 415 Heterogen Atoms 54
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building