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A ThDP-dependent enzyme belonging to the 1-deoxy-D-xylulose-5-phosphate synthase (DXPS)-like subfamily
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, HANGING DROP 289 0.2 M Sodium malonate pH 6.0, 20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.654 α = 90 b = 71.787 β = 97.05 c = 118.447 γ = 90
Symmetry Space Group C 1 2 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 2024-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97954 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.42 48.66 99.77 0.1022 9.2 6.6 46470
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 0.4262 3.45
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 (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 2.42 48.66 44157 2325 99.7 0.1955 0.19225 0.2087 0.25664 0.2626 RANDOM 23.793
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] -0.08 0.01 0.01 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.977 r_dihedral_angle_4_deg 19.149 r_dihedral_angle_3_deg 16.393 r_dihedral_angle_1_deg 7.723 r_long_range_B_refined 5.467 r_long_range_B_other 5.366 r_scangle_other 3.687 r_mcangle_it 2.999 r_mcangle_other 2.999 r_scbond_it 2.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.977 r_dihedral_angle_4_deg 19.149 r_dihedral_angle_3_deg 16.393 r_dihedral_angle_1_deg 7.723 r_long_range_B_refined 5.467 r_long_range_B_other 5.366 r_scangle_other 3.687 r_mcangle_it 2.999 r_mcangle_other 2.999 r_scbond_it 2.363 r_scbond_other 2.293 r_mcbond_it 1.961 r_mcbond_other 1.961 r_angle_refined_deg 1.781 r_angle_other_deg 1.282 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9138 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASES phasing PHENIX refinement