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AcuB from Geobacillus stearothermophilus with ADP 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 2.59 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.433 α = 90 b = 96.513 β = 90 c = 101.157 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 2.53 50 100 0.17 0.999 12.4 13.6 17740 -3 67.4
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 2.53 2.76 100 1.085 0.836 2.4 13.1
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 2.53 48.303 17738 873 99.921 0.195 0.1922 0.1931 0.2434 0.2454 81.911
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] 5.079 -1.788 -3.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.225 r_dihedral_angle_6_deg 14.631 r_lrange_it 12.431 r_lrange_other 12.43 r_scangle_it 10.191 r_scangle_other 10.189 r_mcangle_it 9.14 r_mcangle_other 9.139 r_dihedral_angle_2_deg 8.121 r_scbond_it 7.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.225 r_dihedral_angle_6_deg 14.631 r_lrange_it 12.431 r_lrange_other 12.43 r_scangle_it 10.191 r_scangle_other 10.189 r_mcangle_it 9.14 r_mcangle_other 9.139 r_dihedral_angle_2_deg 8.121 r_scbond_it 7.212 r_scbond_other 7.211 r_dihedral_angle_1_deg 7.2 r_mcbond_it 6.476 r_mcbond_other 6.476 r_angle_refined_deg 1.864 r_angle_other_deg 0.569 r_symmetry_nbd_refined 0.345 r_nbd_other 0.287 r_nbd_refined 0.231 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.149 r_ncsr_local_group_1 0.1 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.079 r_dihedral_angle_other_2_deg 0.076 r_symmetry_xyhbond_nbd_refined 0.075 r_bond_refined_d 0.008 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 3127 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing