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AcuB from Geobacillus stearothermophilus with AMP
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 10 mM AMP
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 = 52.686 α = 90 b = 96.414 β = 90 c = 101.867 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 2024-03-15 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 2.3 50 100 0.276 0.996 11.7 12.9 23740 -3 41.4
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 2.3 2.49 100 1.549 0.537 2 13.6
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 2.3 48.254 23730 1248 99.971 0.202 0.1997 0.2023 0.25 0.2509 45.518
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] 1.02 0.588 -1.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.552 r_dihedral_angle_6_deg 14.292 r_lrange_it 10.72 r_lrange_other 10.68 r_dihedral_angle_2_deg 9.737 r_dihedral_angle_1_deg 7.089 r_scangle_it 6.086 r_scangle_other 6.085 r_mcangle_it 5.479 r_mcangle_other 5.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.552 r_dihedral_angle_6_deg 14.292 r_lrange_it 10.72 r_lrange_other 10.68 r_dihedral_angle_2_deg 9.737 r_dihedral_angle_1_deg 7.089 r_scangle_it 6.086 r_scangle_other 6.085 r_mcangle_it 5.479 r_mcangle_other 5.478 r_scbond_it 3.794 r_scbond_other 3.793 r_mcbond_it 3.495 r_mcbond_other 3.494 r_angle_refined_deg 1.747 r_angle_other_deg 0.553 r_symmetry_xyhbond_nbd_other 0.261 r_symmetry_nbd_refined 0.236 r_nbd_refined 0.221 r_nbd_other 0.217 r_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.121 r_ncsr_local_group_1 0.101 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.076 r_dihedral_angle_other_2_deg 0.015 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 3180 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing