6MWF
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0459
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QHD | PDB entry 3qhd |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Hampton research Index HT screen, condition B7: 1344mM Potassium phosphate dibasic, 56mM sodium phosphate monobasic; BupsA.00122.a.A1.PW28261 BupsA.00122.a.A1.PW28612 at 14.37mg/ml + 9mM compound bsi108635/HGN-0049; Cryo: 15% EG; Tray 300524b7, puck CVW3-4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.03 | α = 90 |
b = 67.93 | β = 96.58 |
c = 60.76 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 100 | CCD | RIGAKU SATURN 944+ | 2018-05-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.75 | 33.661 | 97.6 | 0.098 | 0.114 | 0.997 | 18.95 | 3.037 | 46654 | 23.499 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.75 | 1.8 | 96.5 | 0.448 | 0.606 | 0.705 | 1.91 | 1.91 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3qhd | 1.75 | 33.661 | 1.39 | 46647 | 2016 | 97.6 | 0.1506 | 0.1491 | 0.1842 | 0 | 21.3049 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.672 |
f_angle_d | 0.951 |
f_chiral_restr | 0.063 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3472 |
Nucleic Acid Atoms | |
Solvent Atoms | 459 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Coot | model building |