8H7C
Crystal structure of a de novo enzyme, ferric enterobactin esterase Syn-F4 (K4T) - Pt derivative
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
1.91 | 35.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.986 | α = 90 |
b = 61.468 | β = 90 |
c = 128.991 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.15 | 50 | 8975 | 464 | 88.08 | 0.2347 | 0.2327 | 0.2704 | 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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1576 |
Nucleic Acid Atoms | |
Solvent Atoms | 41 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHENIX | phasing |