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AcuB from Geobacillus stearothermophilus with AMP and ATP
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 ATP
cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.55 51.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.564 α = 90 b = 96.535 β = 90 c = 101.435 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) 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 3.06 50 99.6 0.227 0.997 8.3 12.8 10462 -3 84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.06 50 99.9 1.61 0.657 1.3 13.9
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 THROUGHOUT 3.06 48.314 10027 513 99.741 0.226 0.2232 0.2251 0.2871 0.2896 126.787
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] 15.027 -6.894 -8.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.111 r_lrange_it 13.258 r_lrange_other 13.257 r_dihedral_angle_6_deg 11.603 r_mcangle_it 9.226 r_mcangle_other 9.224 r_scangle_it 8.796 r_scangle_other 8.795 r_dihedral_angle_1_deg 6.706 r_mcbond_it 5.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.111 r_lrange_it 13.258 r_lrange_other 13.257 r_dihedral_angle_6_deg 11.603 r_mcangle_it 9.226 r_mcangle_other 9.224 r_scangle_it 8.796 r_scangle_other 8.795 r_dihedral_angle_1_deg 6.706 r_mcbond_it 5.791 r_mcbond_other 5.789 r_dihedral_angle_2_deg 5.498 r_scbond_it 5.268 r_scbond_other 5.267 r_angle_refined_deg 1.099 r_dihedral_angle_other_2_deg 0.451 r_angle_other_deg 0.365 r_symmetry_xyhbond_nbd_refined 0.251 r_nbd_other 0.225 r_symmetry_nbd_refined 0.22 r_nbd_refined 0.2 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.157 r_ncsr_local_group_1 0.095 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.049 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3137 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing