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Crystal structure of S. aureus HMG-CoA synthase covalently bound to inhibitor
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, SITTING DROP 298 2.7 M Sodium malonate pH 7.0
0.1 M BIS-TRIS propane pH 6.6
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.616 α = 90 b = 58.134 β = 97.499 c = 194.964 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 9M 2026-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 140.385 94 0.931 6.5 2.6 234735
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 0.151
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 FREE R-VALUE 2.05 140.385 234735 11666 93.736 0.227 0.2263 0.2255 0.2503 0.247 44.746
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] 0.523 -1.513 0.394 -0.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.248 r_dihedral_angle_3_deg 13.768 r_lrange_it 8.72 r_lrange_other 8.72 r_dihedral_angle_2_deg 8.019 r_scangle_it 7.204 r_scangle_other 7.204 r_dihedral_angle_1_deg 6.486 r_mcangle_it 6.117 r_mcangle_other 6.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.248 r_dihedral_angle_3_deg 13.768 r_lrange_it 8.72 r_lrange_other 8.72 r_dihedral_angle_2_deg 8.019 r_scangle_it 7.204 r_scangle_other 7.204 r_dihedral_angle_1_deg 6.486 r_mcangle_it 6.117 r_mcangle_other 6.117 r_scbond_it 4.777 r_scbond_other 4.776 r_mcbond_it 4.182 r_mcbond_other 4.182 r_angle_refined_deg 1.562 r_angle_other_deg 0.55 r_symmetry_nbd_refined 0.262 r_nbd_other 0.239 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_other 0.125 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.072 r_ncsr_local_group_22 0.071 r_ncsr_local_group_20 0.07 r_ncsr_local_group_21 0.07 r_ncsr_local_group_9 0.069 r_ncsr_local_group_14 0.067 r_ncsr_local_group_3 0.066 r_ncsr_local_group_19 0.066 r_ncsr_local_group_8 0.06 r_ncsr_local_group_12 0.06 r_ncsr_local_group_10 0.059 r_ncsr_local_group_17 0.058 r_ncsr_local_group_13 0.057 r_ncsr_local_group_4 0.056 r_ncsr_local_group_11 0.056 r_ncsr_local_group_18 0.056 r_ncsr_local_group_24 0.056 r_ncsr_local_group_6 0.055 r_ncsr_local_group_15 0.055 r_ncsr_local_group_2 0.054 r_ncsr_local_group_25 0.053 r_ncsr_local_group_16 0.052 r_ncsr_local_group_28 0.052 r_ncsr_local_group_1 0.051 r_ncsr_local_group_7 0.051 r_ncsr_local_group_26 0.051 r_ncsr_local_group_5 0.05 r_ncsr_local_group_23 0.05 r_ncsr_local_group_27 0.046 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 24334 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing