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Phocaeicola vulgatus sialic acid esterase at 1.44 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 4.5 293 18 % (w/v) PEG 3350, 200 mM sodium malonate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.269 α = 90 b = 90.15 β = 99.289 c = 76.579 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 EIGER2 XE 16M 2021-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.44 70.434 97.7 1 18.3 6.8 168248
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 1.44 1.46 0.712
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 1.44 70.434 168177 8262 97.573 0.178 0.177 0.177 0.203 0.2029 22.426
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] -0.072 0.685 -0.424 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.925 r_dihedral_angle_4_deg 13.982 r_dihedral_angle_3_deg 12.062 r_lrange_it 7.143 r_lrange_other 7.141 r_dihedral_angle_1_deg 6.392 r_scangle_it 4.37 r_scangle_other 4.37 r_scbond_it 2.956 r_scbond_other 2.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.925 r_dihedral_angle_4_deg 13.982 r_dihedral_angle_3_deg 12.062 r_lrange_it 7.143 r_lrange_other 7.141 r_dihedral_angle_1_deg 6.392 r_scangle_it 4.37 r_scangle_other 4.37 r_scbond_it 2.956 r_scbond_other 2.955 r_mcangle_it 2.526 r_mcangle_other 2.525 r_mcbond_it 1.853 r_mcbond_other 1.848 r_angle_refined_deg 1.835 r_angle_other_deg 1.529 r_symmetry_nbd_refined 0.276 r_nbd_refined 0.229 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.175 r_symmetry_nbd_other 0.17 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.1 r_symmetry_xyhbond_nbd_other 0.092 r_symmetry_nbtor_other 0.078 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 6350 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing