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Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-acetylneuraminic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.8 M sodium formate, 12% PEG 4000, 0.1 M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.262 α = 90 b = 79.017 β = 94.83 c = 112.935 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 PIXEL DECTRIS EIGER X 16M 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.7001 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 49.75 100 0.293 0.302 0.071 0.993 10.3 18 76209
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 100 1.927 1.983 0.466 0.71 17.7
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 6RZD 2 49.8 72411 3779 99.95 0.2116 0.2095 0.2201 0.2517 0.2601 RANDOM 23.084
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] 0.5 -0.46 0.17 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.437 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 7.453 r_angle_refined_deg 1.829 r_angle_other_deg 1.366 r_chiral_restr 0.213 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.437 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 7.453 r_angle_refined_deg 1.829 r_angle_other_deg 1.366 r_chiral_restr 0.213 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8016 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement DIALS data collection Aimless data scaling PHASER phasing DIALS data reduction