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Crystal structure of monoalkyl phthalate hydrolase from Rhodococcus sp. EG-5
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, 0.01M BARIUM CHLORIDE DI HYDRATE, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.612 α = 90 b = 245.492 β = 90 c = 191.658 γ = 90
Symmetry Space Group C 2 2 2
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 2023-05-25 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 3 27.38 99.72 0.947 11.23 11.23 83596
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 3 3.107 0.885
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 3 27.38 83568 4208 99.72 0.254 0.2514 0.2423 0.2944 0.2828 17.385
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] 2.734 6.467 -9.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.598 r_dihedral_angle_6_deg 13.756 r_dihedral_angle_2_deg 10.8 r_dihedral_angle_1_deg 6.556 r_lrange_it 3.895 r_lrange_other 3.895 r_mcangle_it 2.501 r_mcangle_other 2.501 r_scangle_it 2.431 r_scangle_other 2.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.598 r_dihedral_angle_6_deg 13.756 r_dihedral_angle_2_deg 10.8 r_dihedral_angle_1_deg 6.556 r_lrange_it 3.895 r_lrange_other 3.895 r_mcangle_it 2.501 r_mcangle_other 2.501 r_scangle_it 2.431 r_scangle_other 2.431 r_mcbond_it 1.546 r_mcbond_other 1.546 r_scbond_it 1.479 r_scbond_other 1.479 r_angle_refined_deg 1.438 r_angle_other_deg 0.476 r_symmetry_xyhbond_nbd_refined 0.359 r_xyhbond_nbd_other 0.281 r_symmetry_nbd_refined 0.232 r_nbd_refined 0.224 r_nbd_other 0.224 r_symmetry_nbd_other 0.214 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.18 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21922 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing