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AcuB from Geobacillus stearothermophilus with Ap4A
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 over night in 10 mM Ap4A
cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.61 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.295 α = 90 b = 96.954 β = 90 c = 101.709 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 2025-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 3.35 50 100 0.433 0.99 8 12.7 7877 -3 61.2
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 3.35 50 100 1.57 0.61 2 12.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.35 48.524 7865 402 99.975 0.231 0.2288 0.2328 0.2617 0.2687 83.038
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] 5.183 -3.01 -2.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.737 r_dihedral_angle_6_deg 11.017 r_lrange_it 5.387 r_lrange_other 5.387 r_dihedral_angle_1_deg 4.875 r_dihedral_angle_2_deg 4.231 r_scangle_it 3.076 r_scangle_other 3.075 r_mcangle_it 2.901 r_mcangle_other 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.737 r_dihedral_angle_6_deg 11.017 r_lrange_it 5.387 r_lrange_other 5.387 r_dihedral_angle_1_deg 4.875 r_dihedral_angle_2_deg 4.231 r_scangle_it 3.076 r_scangle_other 3.075 r_mcangle_it 2.901 r_mcangle_other 2.9 r_scbond_it 1.696 r_scbond_other 1.696 r_mcbond_it 1.638 r_mcbond_other 1.638 r_angle_refined_deg 0.849 r_angle_other_deg 0.309 r_dihedral_angle_other_2_deg 0.284 r_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.172 r_nbd_other 0.171 r_symmetry_nbd_other 0.17 r_symmetry_nbd_refined 0.162 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.125 r_ncsr_local_group_1 0.1 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.041 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3147 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing