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AcuB from Geobacillus stearothermophilus without nucleotide
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 4041A1
10% PEG 20000, 100 mM MES pH 6.5,
cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.21 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.618 α = 90 b = 96.777 β = 90 c = 98.97 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 2025-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0596 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) Rpim 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 50 100 0.109 0.113 0.031 0.999 20.7 13.1 30440 -3 35.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 1.176 1.224 0.338 0.82 2.8 12.8
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 48.435 30382 1465 99.977 0.193 0.1906 0.1923 0.2447 0.2468 38.967
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] 3.558 -1.932 -1.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.014 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_6_deg 13.777 r_lrange_it 8.743 r_lrange_other 8.737 r_scangle_it 6.512 r_scangle_other 6.511 r_dihedral_angle_1_deg 6.407 r_mcangle_it 4.772 r_mcangle_other 4.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.014 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_6_deg 13.777 r_lrange_it 8.743 r_lrange_other 8.737 r_scangle_it 6.512 r_scangle_other 6.511 r_dihedral_angle_1_deg 6.407 r_mcangle_it 4.772 r_mcangle_other 4.772 r_scbond_it 4.232 r_scbond_other 4.23 r_mcbond_it 3.202 r_mcbond_other 3.201 r_angle_refined_deg 1.91 r_angle_other_deg 0.614 r_nbd_refined 0.238 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.182 r_nbd_other 0.171 r_symmetry_xyhbond_nbd_refined 0.153 r_ncsr_local_group_1 0.142 r_symmetry_nbd_refined 0.131 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3190 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing