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Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with propylene glycol
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 pH7.0
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.708 α = 90 b = 137.45 β = 90 c = 190.309 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 2026-01-27 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 2.8 28.542 99.61 0.994 38.3 20.9 20682
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 2.8 2.9 0.977
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 2.8 28.542 20658 1044 99.643 0.244 0.2423 0.2402 0.2836 0.2819 53.426
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] -1.611 -4.274 5.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.275 r_dihedral_angle_6_deg 12.875 r_dihedral_angle_2_deg 8.24 r_dihedral_angle_1_deg 8.113 r_lrange_it 4.429 r_lrange_other 4.428 r_mcangle_it 2.762 r_mcangle_other 2.762 r_scangle_it 2.344 r_scangle_other 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.275 r_dihedral_angle_6_deg 12.875 r_dihedral_angle_2_deg 8.24 r_dihedral_angle_1_deg 8.113 r_lrange_it 4.429 r_lrange_other 4.428 r_mcangle_it 2.762 r_mcangle_other 2.762 r_scangle_it 2.344 r_scangle_other 2.344 r_angle_refined_deg 1.715 r_mcbond_it 1.599 r_mcbond_other 1.599 r_scbond_it 1.335 r_scbond_other 1.335 r_angle_other_deg 0.635 r_symmetry_xyhbond_nbd_refined 0.276 r_nbd_refined 0.232 r_symmetry_nbd_other 0.206 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.187 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.136 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_3 0.079 r_ncsr_local_group_5 0.079 r_ncsr_local_group_6 0.073 r_ncsr_local_group_2 0.067 r_ncsr_local_group_4 0.065 r_ncsr_local_group_1 0.059 r_symmetry_xyhbond_nbd_other 0.016 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 6548 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing