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Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8H7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris, 0.2M ammonium acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.91 35.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.986 α = 90 b = 61.928 β = 90 c = 127.639 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 95 CCD ADSC QUANTUM 270 2017-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 50 99.9 0.142 0.147 0.04 6.1 13.3 10016
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.952 0.995 0.285 0.845 11.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8H7C 2.2 50 9499 472 99.72 0.24845 0.24565 0.2486 0.30255 0.2994 RANDOM 59.446
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] -3.74 -2.95 6.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.034 r_dihedral_angle_3_deg 17.103 r_dihedral_angle_4_deg 16.611 r_long_range_B_refined 9.921 r_long_range_B_other 9.918 r_scangle_other 7.451 r_mcangle_it 5.564 r_mcangle_other 5.562 r_dihedral_angle_1_deg 5.538 r_scbond_it 4.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.034 r_dihedral_angle_3_deg 17.103 r_dihedral_angle_4_deg 16.611 r_long_range_B_refined 9.921 r_long_range_B_other 9.918 r_scangle_other 7.451 r_mcangle_it 5.564 r_mcangle_other 5.562 r_dihedral_angle_1_deg 5.538 r_scbond_it 4.78 r_scbond_other 4.777 r_mcbond_other 3.872 r_mcbond_it 3.868 r_angle_refined_deg 1.325 r_angle_other_deg 0.935 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1585 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing