2QKF
Crystal structure 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 | 1D9E | PDB ENTRY 1D9E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 4.6 | 295 | CRYSTALLISATION CONDITIONS: 18.6 MG/ML PROTEIN MIXED 1:1 WITH RESERVOIR LIQUOR CONTAINING 100 MM SODIUM ACETATE PH 4.60, 200 MICROMOLAR PEP, 0.6, 1.6 MOLAR SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.515 | α = 90 |
b = 85.295 | β = 90 |
c = 162.686 | 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 | OSMIC BLUE MIRRORS | 2005-11-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 |
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 | 1.75 | 40 | 97 | 0.043 | 13.4 | 3.95 | 111333 | 31.7 |
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 | 1.75 | 1.81 | 78.2 | 0.368 | 2.7 | 4.16 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1D9E | 1.75 | 40 | 111333 | 105744 | 5588 | 97 | 0.197 | 0.196 | 0.235 | RANDOM | 30.27 |
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] | |
0.91 | 0.2 | -1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.994 |
r_dihedral_angle_4_deg | 17.825 |
r_dihedral_angle_3_deg | 13.796 |
r_dihedral_angle_1_deg | 5.619 |
r_mcangle_it | 2.874 |
r_mcbond_it | 1.869 |
r_scangle_it | 1.683 |
r_angle_refined_deg | 1.306 |
r_scbond_it | 1.041 |
r_angle_other_deg | 0.817 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7748 |
Nucleic Acid Atoms | |
Solvent Atoms | 528 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |
MOLREP | phasing |