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Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Thermus thermophilus HB27 complexed to NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q72J81-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 LiNaK
Buffer System 5 pH = 7.5
Precipitant Mix 5, both the Buffer System 5 and the Precipitant Mix 5 are available at Molecular Dimensions website
Crystal Properties Matthews coefficient Solvent content 3.09 60.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.202 α = 90 b = 148.289 β = 111.08 c = 97.442 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 PILATUS3 S 6M 2023-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 20 99.8 0.05 0.999 11.7 4 212528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.6 1.628 0.459 0.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 19.93 203949 8537 99.74 0.20066 0.19959 0.2067 0.22601 0.2318 RANDOM 52.143
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] -2.05 1.7 -3.39 3.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.523 r_dihedral_angle_4_deg 19.689 r_dihedral_angle_3_deg 16.239 r_long_range_B_other 9.419 r_long_range_B_refined 9.414 r_scangle_other 7.931 r_dihedral_angle_1_deg 6.159 r_mcangle_it 5.441 r_mcangle_other 5.441 r_scbond_it 5.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.523 r_dihedral_angle_4_deg 19.689 r_dihedral_angle_3_deg 16.239 r_long_range_B_other 9.419 r_long_range_B_refined 9.414 r_scangle_other 7.931 r_dihedral_angle_1_deg 6.159 r_mcangle_it 5.441 r_mcangle_other 5.441 r_scbond_it 5.377 r_scbond_other 5.377 r_mcbond_it 4.188 r_mcbond_other 4.187 r_angle_refined_deg 1.526 r_angle_other_deg 1.333 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13301 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing