☰ Navigation Tabs
Crystal structure of Cysteine-dependent hydrolase (CsdH) from Rhodococcus opacus in complex with 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 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 2026-05-06 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 99.29 0.994 22.19 6.6 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 28.54 18136 906 99.354 0.194 0.192 0.192 0.2402 0.2408 53.193
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] 0.027 -0.239 0.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.519 r_dihedral_angle_6_deg 12.686 r_dihedral_angle_2_deg 9.386 r_dihedral_angle_1_deg 7.853 r_lrange_it 4.818 r_lrange_other 4.817 r_mcangle_it 2.607 r_mcangle_other 2.606 r_scangle_it 2.521 r_scangle_other 2.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.519 r_dihedral_angle_6_deg 12.686 r_dihedral_angle_2_deg 9.386 r_dihedral_angle_1_deg 7.853 r_lrange_it 4.818 r_lrange_other 4.817 r_mcangle_it 2.607 r_mcangle_other 2.606 r_scangle_it 2.521 r_scangle_other 2.521 r_mcbond_it 1.511 r_mcbond_other 1.511 r_angle_refined_deg 1.499 r_scbond_it 1.436 r_scbond_other 1.436 r_angle_other_deg 0.533 r_symmetry_xyhbond_nbd_other 0.389 r_symmetry_xyhbond_nbd_refined 0.241 r_nbd_refined 0.229 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.177 r_nbd_other 0.169 r_symmetry_nbd_refined 0.159 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_2 0.068 r_ncsr_local_group_3 0.068 r_chiral_restr 0.067 r_ncsr_local_group_1 0.062 r_ncsr_local_group_4 0.062 r_ncsr_local_group_5 0.059 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 26 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing