6V3M
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)
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 | 290 | Bups122_opt3 screen: 100mM HEPES free acid / NaOH pH 7.4, 200mM ammonium acetate, 27% (w/V) PEG 3350: BupsA.00122.a.A1.PW28612 at 14.33mg/ml plus 1mM ZnCl2 and 10mM compound HGN-0961/BSI110840: soaked over night with reservoir and 25mM compound: cryo: 20% EG + soak buffer: tray 310506a10: puck bno0-4. The ligand description was generated from a smiles string using phenix elbow. The ligand structure was minimized using GAMESS with the 3-21G basis. Restraints were extracted using phenix.elbow |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.31 | α = 90 |
b = 67.55 | β = 96.317 |
c = 60.57 | 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+ | 2019-11-07 | 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 | 1.55 | 50 | 98.5 | 0.026 | 0.027 | 1 | 49.7 | 11.388 | 67221 | 23.959 |
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 | 1.55 | 1.59 | 93.2 | 0.32 | 0.36 | 0.941 | 4.47 | 4.565 |
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 | FREE R-VALUE | PDB entry 3qhd | 1.55 | 44.39 | 1.34 | 67208 | 1897 | 98.47 | 0.1454 | 0.1447 | 0.1693 | 0 | 23.76 |
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 | 20.1948 |
f_angle_d | 1.1692 |
f_chiral_restr | 0.0764 |
f_bond_d | 0.0104 |
f_plane_restr | 0.0066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3519 |
Nucleic Acid Atoms | |
Solvent Atoms | 465 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | phasing |