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Listeria monocytogenes GT108 family enzyme, native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M NH4NO3 and 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.432 α = 90 b = 75.726 β = 99.378 c = 78.508 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 2020-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.41 54.15 99.3 0.116 0.139 0.075 0.997 4.8 6.2 113781
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) 1.41 1.43 86.6 2.299 2.853 1.665 0.324 0.1 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.41 54.148 111992 5513 97.966 0.219 0.2179 0.2249 0.2484 0.2535 22.96
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] 1.524 -2.139 -0.535 -0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.682 r_dihedral_angle_3_deg 12.689 r_dihedral_angle_2_deg 12.066 r_dihedral_angle_1_deg 7.438 r_lrange_it 6.883 r_lrange_other 6.86 r_scangle_other 5.217 r_scangle_it 5.213 r_mcangle_it 3.75 r_mcangle_other 3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.682 r_dihedral_angle_3_deg 12.689 r_dihedral_angle_2_deg 12.066 r_dihedral_angle_1_deg 7.438 r_lrange_it 6.883 r_lrange_other 6.86 r_scangle_other 5.217 r_scangle_it 5.213 r_mcangle_it 3.75 r_mcangle_other 3.75 r_scbond_other 3.534 r_scbond_it 3.531 r_mcbond_it 2.647 r_mcbond_other 2.647 r_angle_refined_deg 1.974 r_angle_other_deg 0.833 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.193 r_nbd_other 0.18 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_refined 0.144 r_ncsr_local_group_1 0.129 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.012 r_bond_other_d 0.003 r_gen_planes_refined 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4753 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling DIALS data reduction