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AcuB from Geobacillus stearothermophilus with AMP and ADP
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 293 10% PEG 20000, 100 mM MES pH 6.5,
soaked 30 min in 5 mM AMP + 5 mM ADP
cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.59 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.298 α = 90 b = 96.668 β = 90 c = 101.381 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M double mirror 2025-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.05960 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.62 50 97.5 0.071 0.074 0.999 21 12.7 15706 -3 72.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.78 84.6 0.702 0.745 0.838 2.22 8.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.62 48.381 15660 808 97.655 0.184 0.1814 0.2353 0.2308 78.689
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] 4.934 -0.564 -4.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.13 r_dihedral_angle_6_deg 14.315 r_lrange_it 11.352 r_lrange_other 11.325 r_scangle_it 9.61 r_scangle_other 9.608 r_dihedral_angle_2_deg 8.622 r_mcangle_it 7.644 r_mcangle_other 7.644 r_scbond_it 6.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.13 r_dihedral_angle_6_deg 14.315 r_lrange_it 11.352 r_lrange_other 11.325 r_scangle_it 9.61 r_scangle_other 9.608 r_dihedral_angle_2_deg 8.622 r_mcangle_it 7.644 r_mcangle_other 7.644 r_scbond_it 6.712 r_scbond_other 6.71 r_dihedral_angle_1_deg 6.451 r_mcbond_it 5.575 r_mcbond_other 5.575 r_angle_refined_deg 1.701 r_angle_other_deg 0.544 r_symmetry_nbd_refined 0.285 r_nbd_other 0.26 r_nbd_refined 0.24 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.131 r_ncsr_local_group_1 0.106 r_dihedral_angle_other_2_deg 0.097 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing