☰ Navigation Tabs
Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) - Pt derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 293 0.1M Tris, 0.2M ammonium acetate, 8% PEG 3350
(soaking in 10mM K2PtCl4 for 1 day)
Crystal Properties Matthews coefficient Solvent content 1.91 35.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.986 α = 90 b = 61.468 β = 90 c = 128.991 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 2018-11-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.073, 1.069, 1.045 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 2.15 50 95.5 0.075 0.078 0.022 5.5 11.7 10257
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 2.15 2.19 71.6 0.5 0.532 0.174 0.922 7.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.15 50 8975 464 88.08 0.2347 0.2327 0.241 0.2704 0.2724 RANDOM 35.834
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] -0.02 -0.13 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.711 r_dihedral_angle_3_deg 18.186 r_dihedral_angle_4_deg 15.645 r_dihedral_angle_1_deg 5.206 r_angle_refined_deg 1.265 r_angle_other_deg 0.926 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.711 r_dihedral_angle_3_deg 18.186 r_dihedral_angle_4_deg 15.645 r_dihedral_angle_1_deg 5.206 r_angle_refined_deg 1.265 r_angle_other_deg 0.926 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1576 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing