4JTL
Crystal structure of F139G mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2QKF | PDB entry 2QKF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 297 | 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl, cryoprotectant solution, comprising 20% glycerol and reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.997 | α = 90 |
b = 85.924 | β = 90 |
c = 163.37 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 120 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2010-02-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.1 | 38.06 | 92 | 0.08 | 7.2 | 3.12 | 62633 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.1 | 2.18 | 99.9 | 0.395 | 2.3 | 3.08 | 6692 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2QKF | 2.1 | 37.09 | 62592 | 3143 | 91.78 | 0.2186 | 0.217 | 0.2499 | RANDOM | 40.4761 |
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] | |
0.09 | 1.42 | -1.51 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.875 |
r_dihedral_angle_4_deg | 18.016 |
r_dihedral_angle_3_deg | 15.753 |
r_dihedral_angle_1_deg | 5.919 |
r_mcangle_it | 4.041 |
r_mcbond_it | 2.807 |
r_mcbond_other | 2.807 |
r_angle_refined_deg | 1.709 |
r_angle_other_deg | 1.507 |
r_chiral_restr | 0.095 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7759 |
Nucleic Acid Atoms | |
Solvent Atoms | 130 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
d*TREK | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |