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Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with Catechol
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 7.4 293 0.1M Sodium Fluoride pH 7.4
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 2026-02-20 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 28.54 99.28 0.993 22.18 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 3.005 0.93
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 NONE 2.9 28.54 18136 906 99.354 0.195 0.1921 0.1921 0.2426 0.2431 53.58
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] 0.058 -0.045 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.373 r_dihedral_angle_6_deg 12.592 r_dihedral_angle_2_deg 9.143 r_dihedral_angle_1_deg 7.811 r_lrange_it 4.683 r_lrange_other 4.681 r_mcangle_it 2.53 r_mcangle_other 2.529 r_scangle_it 2.462 r_scangle_other 2.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.373 r_dihedral_angle_6_deg 12.592 r_dihedral_angle_2_deg 9.143 r_dihedral_angle_1_deg 7.811 r_lrange_it 4.683 r_lrange_other 4.681 r_mcangle_it 2.53 r_mcangle_other 2.529 r_scangle_it 2.462 r_scangle_other 2.462 r_angle_refined_deg 1.481 r_mcbond_it 1.466 r_mcbond_other 1.465 r_scbond_it 1.405 r_scbond_other 1.405 r_angle_other_deg 0.525 r_symmetry_xyhbond_nbd_other 0.378 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.179 r_nbd_other 0.173 r_symmetry_nbd_refined 0.16 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_2 0.068 r_chiral_restr 0.066 r_ncsr_local_group_3 0.066 r_ncsr_local_group_1 0.063 r_ncsr_local_group_4 0.062 r_ncsr_local_group_5 0.058 r_ncsr_local_group_6 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 25 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing