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GT108 family enzyme from Chlamydia abortus in complex with mannose-1-phosphate (M1P)
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 NH4Cl, 0.1 M MES pH 5.8 and 24% (w/v) PEG 6000 soaking with 5mM M1P
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.182 α = 90 b = 163.04 β = 117.34 c = 51.165 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 2020-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.980 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 1.68 163.04 98.7 0.061 0.072 0.038 0.999 11.2 6.6 78480
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) 1.68 1.71 82.3 1.658 2.056 1.195 0.329 0.7 4.9
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 1.68 81.52 78398 3947 98.651 0.193 0.1912 0.2004 0.2247 0.2321 39.214
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] -0.73 0.505 -2.528 1.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.998 r_dihedral_angle_3_deg 12.219 r_dihedral_angle_2_deg 9.177 r_lrange_it 8.239 r_lrange_other 8.238 r_dihedral_angle_1_deg 7.475 r_scangle_it 7.22 r_scangle_other 7.172 r_mcangle_it 5.32 r_mcangle_other 5.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.998 r_dihedral_angle_3_deg 12.219 r_dihedral_angle_2_deg 9.177 r_lrange_it 8.239 r_lrange_other 8.238 r_dihedral_angle_1_deg 7.475 r_scangle_it 7.22 r_scangle_other 7.172 r_mcangle_it 5.32 r_mcangle_other 5.32 r_scbond_it 5.305 r_scbond_other 5.246 r_mcbond_it 4.306 r_mcbond_other 4.301 r_angle_refined_deg 2.009 r_angle_other_deg 0.702 r_nbd_other 0.223 r_symmetry_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.215 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.09 r_ncsr_local_group_1 0.072 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.013 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4882 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling DIALS data reduction