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AcuB from Geobacillus stearothermophilus with 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 in 10 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 = 52.486 α = 90 b = 96.492 β = 90 c = 101.088 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 PILATUS3 6M 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 2.76 50 99.5 0.128 0.998 12.8 6.9 26470 -3 63.7
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 2.76 3.02 99.3 0.527 0.906 2.8 6.8
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 2.76 48.293 13752 631 99.964 0.186 0.1828 0.1808 0.2489 0.2469 70.457
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] 6.752 -2.871 -3.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.369 r_dihedral_angle_6_deg 13.243 r_lrange_it 10.366 r_lrange_other 10.355 r_dihedral_angle_2_deg 8.504 r_scangle_it 8.289 r_scangle_other 8.288 r_mcangle_it 7.031 r_mcangle_other 7.03 r_dihedral_angle_1_deg 6.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.369 r_dihedral_angle_6_deg 13.243 r_lrange_it 10.366 r_lrange_other 10.355 r_dihedral_angle_2_deg 8.504 r_scangle_it 8.289 r_scangle_other 8.288 r_mcangle_it 7.031 r_mcangle_other 7.03 r_dihedral_angle_1_deg 6.98 r_scbond_it 5.719 r_scbond_other 5.717 r_mcbond_it 4.795 r_mcbond_other 4.782 r_angle_refined_deg 1.755 r_angle_other_deg 0.553 r_symmetry_nbd_refined 0.315 r_nbd_other 0.27 r_nbd_refined 0.245 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.152 r_ncsr_local_group_1 0.108 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_dihedral_angle_other_2_deg 0.005 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 10 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing