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AcuB from Bacillus subtilis with AMP and 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 protein (13 mg/mL, with 1 mM AMP) +
5% MPD, 5% ethanol, 100 mM HEPES pH 7.5,
cryo: 20% MPD, 5% ethanol, 100 mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.305 α = 90 b = 79.779 β = 90 c = 153.788 γ = 90
Symmetry Space Group P 21 2 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 2024-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.97624 EMBL/DESY, HAMBURG X13
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 2.64 50 97.4 0.137 0.145 0.063 0.998 10 10 24477 -3 73.6
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 2.64 2.77 99.2 2.437 2.602 0.8 0.64 1.1 10.3
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 2.64 48.79 24436 1214 97.417 0.209 0.2067 0.2039 0.2664 0.265 100.062
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] -4.31 6.001 -1.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.598 r_dihedral_angle_6_deg 13.159 r_lrange_it 11.391 r_lrange_other 11.39 r_scangle_it 7.915 r_scangle_other 7.914 r_mcangle_it 7.499 r_mcangle_other 7.498 r_dihedral_angle_2_deg 7.289 r_dihedral_angle_1_deg 6.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.598 r_dihedral_angle_6_deg 13.159 r_lrange_it 11.391 r_lrange_other 11.39 r_scangle_it 7.915 r_scangle_other 7.914 r_mcangle_it 7.499 r_mcangle_other 7.498 r_dihedral_angle_2_deg 7.289 r_dihedral_angle_1_deg 6.884 r_scbond_it 4.859 r_scbond_other 4.859 r_mcbond_it 4.661 r_mcbond_other 4.66 r_angle_refined_deg 1.359 r_angle_other_deg 0.461 r_nbd_refined 0.206 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.159 r_nbd_other 0.152 r_ncsr_local_group_1 0.137 r_symmetry_nbd_refined 0.126 r_ncsr_local_group_2 0.121 r_dihedral_angle_other_2_deg 0.119 r_ncsr_local_group_3 0.118 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.01 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5096 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction XSCALE data scaling Aimless data scaling PHASER phasing