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Phocaeicola vulgatus sialic acid esterase at 2.06 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulphate, 0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.233 α = 90 b = 93.233 β = 90 c = 353.623 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 PIXEL DECTRIS EIGER2 X 16M 2021-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.06 80.74 100 0.998 11.2 20.5 106903
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.06 2.1 0.54
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6njc 2.06 80.742 106769 5355 99.988 0.187 0.185 0.1907 0.2258 0.229 37.958
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] -0.037 -0.037 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.977 r_dihedral_angle_4_deg 16.72 r_dihedral_angle_3_deg 16.037 r_dihedral_angle_1_deg 7.614 r_lrange_it 6.546 r_lrange_other 6.546 r_scangle_it 5.054 r_scangle_other 5.051 r_mcangle_it 4.566 r_mcangle_other 4.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.977 r_dihedral_angle_4_deg 16.72 r_dihedral_angle_3_deg 16.037 r_dihedral_angle_1_deg 7.614 r_lrange_it 6.546 r_lrange_other 6.546 r_scangle_it 5.054 r_scangle_other 5.051 r_mcangle_it 4.566 r_mcangle_other 4.566 r_scbond_it 3.606 r_scbond_other 3.602 r_mcbond_it 3.517 r_mcbond_other 3.517 r_angle_refined_deg 1.646 r_angle_other_deg 1.32 r_nbd_refined 0.218 r_nbd_other 0.209 r_symmetry_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.196 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_other 0.099 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12619 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing