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Bifunctional cyclohexadienyl dehydratase/chorismate mutase from Janthinobacterium sp. HH01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HPQ cyclohexadienyl dehydratase from Pseudomonas aeruginosa experimental model PDB 6CNZ chorismate mutase from Burkholderia thailandesis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 10% w/v PEG 20 000
20% v/v PEG MME 550
0.03 M Sodium nitrate
0.03 M Disodium hydrogen phosphate
0.03 M Ammonium sulfate
0.1 M MES/imidazole pH 6.5 (Morpheus buffer 1)
3.5 mg/mL protein in 20 mM TRIS-HCl, pH 8
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.584 α = 90 b = 73.985 β = 90 c = 131.22 γ = 90
Symmetry Space Group P 21 21 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 DECTRIS EIGER X 16M 2019-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
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 1.65 65.6 93 0.998 14.1 12.7 35076
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 1.65 1.83 54.6 0.542 1.6 9.9
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 FREE R-VALUE 1.65 65.6 35076 1717 72.148 0.194 0.1917 0.2015 0.2453 0.2483 28.766
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] -0.076 0.113 -0.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.359 r_dihedral_angle_6_deg 15.212 r_dihedral_angle_2_deg 10.515 r_dihedral_angle_1_deg 6.372 r_lrange_it 6.306 r_lrange_other 6.306 r_scangle_it 5.382 r_scangle_other 5.381 r_mcangle_it 3.874 r_mcangle_other 3.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.359 r_dihedral_angle_6_deg 15.212 r_dihedral_angle_2_deg 10.515 r_dihedral_angle_1_deg 6.372 r_lrange_it 6.306 r_lrange_other 6.306 r_scangle_it 5.382 r_scangle_other 5.381 r_mcangle_it 3.874 r_mcangle_other 3.874 r_scbond_it 3.609 r_scbond_other 3.609 r_mcbond_it 2.916 r_mcbond_other 2.91 r_angle_refined_deg 1.658 r_angle_other_deg 0.545 r_symmetry_xyhbond_nbd_other 0.405 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.222 r_nbd_other 0.215 r_xyhbond_nbd_refined 0.201 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.11 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3066 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing