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Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with Monobutylphthalate (MBP)
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 7 293 0.1M sodium malonate pH 7.0
20%peg 3350
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.285 α = 90 b = 136.51 β = 90 c = 188.382 γ = 90
Symmetry Space Group C 2 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 RIGAKU HyPix-6000HE 2026-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 2.9 28.524 99.29 0.994 22.19 6.5 18141
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 2.9 3.004 0.931
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 NONE AlphaFold 2.9 28.524 18136 906 99.354 0.194 0.1917 0.1876 0.2468 0.2414 51.981
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] -3.351 5.025 -1.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.851 r_dihedral_angle_6_deg 12.858 r_dihedral_angle_2_deg 9.545 r_dihedral_angle_1_deg 8.035 r_lrange_it 5.392 r_lrange_other 5.391 r_scangle_it 3.083 r_scangle_other 3.082 r_mcangle_it 3.017 r_mcangle_other 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.851 r_dihedral_angle_6_deg 12.858 r_dihedral_angle_2_deg 9.545 r_dihedral_angle_1_deg 8.035 r_lrange_it 5.392 r_lrange_other 5.391 r_scangle_it 3.083 r_scangle_other 3.082 r_mcangle_it 3.017 r_mcangle_other 3.017 r_scbond_it 1.789 r_scbond_other 1.788 r_mcbond_it 1.775 r_mcbond_other 1.775 r_angle_refined_deg 1.58 r_angle_other_deg 0.557 r_symmetry_xyhbond_nbd_other 0.369 r_nbd_refined 0.248 r_symmetry_xyhbond_nbd_refined 0.232 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.205 r_nbd_other 0.186 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.167 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_3 0.072 r_chiral_restr 0.069 r_ncsr_local_group_2 0.069 r_ncsr_local_group_1 0.064 r_ncsr_local_group_4 0.063 r_ncsr_local_group_5 0.063 r_ncsr_local_group_6 0.059 r_bond_refined_d 0.007 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 6547 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing