4IPI
Crystal Structure of R314A N-acetyl Neuraminic Acid Synthase from Neiserria meningitidis with Malate bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XUZ | PDB ENTRY 1XUZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 298.15 | 1.7 M malic acid, 10 mM magnesium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58 | α = 90 |
b = 75.8 | β = 90 |
c = 77.52 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | ADSC QUANTUM 315r | 2011-02-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95369 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 27.16 | 100 | 0.106 | 0.106 | 21.7 | 13.9 | 35170 | 35169 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.75 | 1.84 | 100 | 0.508 | 0.508 | 5.2 | 12.9 |
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 1XUZ | 1.75 | 27.16 | 31594 | 3541 | 99.9 | 0.16491 | 0.16132 | 0.1972 | RANDOM | 10.119 |
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] | |
0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.52 |
r_dihedral_angle_4_deg | 22.022 |
r_dihedral_angle_3_deg | 12.55 |
r_dihedral_angle_1_deg | 5.449 |
r_scangle_it | 2.517 |
r_scbond_it | 1.49 |
r_angle_refined_deg | 1.11 |
r_angle_other_deg | 0.81 |
r_mcangle_it | 0.802 |
r_mcbond_it | 0.409 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2692 |
Nucleic Acid Atoms | |
Solvent Atoms | 355 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
CCP4 | model building |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
CCP4 | phasing |