☰ Navigation Tabs
Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with degradation products of diethyl phthalate
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 293 0.1M sodium malonate pH 7.0
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-3000 2026-04-16 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 28.11 99.6 0.994 41.45 20 18637
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 0.984
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 28.11 18619 531 99.673 0.24 0.2394 0.2379 0.263 0.2664 51.987
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] -1.599 -3.846 5.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.882 r_dihedral_angle_6_deg 13.937 r_dihedral_angle_2_deg 10.368 r_dihedral_angle_1_deg 7.935 r_lrange_it 4.554 r_scangle_it 2.151 r_mcangle_it 2.143 r_angle_refined_deg 1.909 r_scbond_it 1.248 r_mcbond_it 1.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.882 r_dihedral_angle_6_deg 13.937 r_dihedral_angle_2_deg 10.368 r_dihedral_angle_1_deg 7.935 r_lrange_it 4.554 r_scangle_it 2.151 r_mcangle_it 2.143 r_angle_refined_deg 1.909 r_scbond_it 1.248 r_mcbond_it 1.235 r_nbtor_refined 0.317 r_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_refined 0.215 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.144 r_ncsr_local_group_1 0.077 r_ncsr_local_group_4 0.077 r_ncsr_local_group_2 0.076 r_ncsr_local_group_3 0.071 r_ncsr_local_group_5 0.071 r_ncsr_local_group_6 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6594 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing