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Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) at 2.0 angstrom resolution
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 8.9 293 0.1M Tris, 0.2M ammonium acetate, 15% PEG 3350 (After crystallization, ferric enterobactin was added.)
Crystal Properties Matthews coefficient Solvent content 1.98 37.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.342 α = 90 b = 61.391 β = 90 c = 135.729 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 PIXEL DECTRIS PILATUS3 S 6M Focusing Mirror 2019-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 50 88.3 0.104 0.109 0.031 5.4 11.6 12201
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 2.03 59.9 0.664 0.701 0.218 0.839 9.6
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 50 9988 538 76.38 0.21967 0.21714 0.2222 0.26624 0.2672 RANDOM 35.875
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] -0.05 -0.45 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.735 r_dihedral_angle_3_deg 16.696 r_dihedral_angle_4_deg 16.636 r_long_range_B_refined 6.553 r_long_range_B_other 6.544 r_dihedral_angle_1_deg 4.724 r_scangle_other 4.255 r_angle_other_deg 3.523 r_mcangle_other 3.209 r_mcangle_it 3.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.735 r_dihedral_angle_3_deg 16.696 r_dihedral_angle_4_deg 16.636 r_long_range_B_refined 6.553 r_long_range_B_other 6.544 r_dihedral_angle_1_deg 4.724 r_scangle_other 4.255 r_angle_other_deg 3.523 r_mcangle_other 3.209 r_mcangle_it 3.204 r_scbond_it 2.514 r_scbond_other 2.513 r_mcbond_it 1.983 r_mcbond_other 1.968 r_angle_refined_deg 1.235 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_gen_planes_refined 0.005 r_bond_other_d 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 1567 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing