2YPP
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with 3 tyrosine molecules
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NV8 | PDB ENTRY 3NV8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.92 | 68.6 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 203.449 | ¦Á = 90 |
b = 203.449 | ¦Â = 90 |
c = 66.49 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 32 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 | ADSC CCD | 2011-08-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 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 | 2.3 | 47.03 | 97 | 0.13 | 0.126 | 10.7 | 7.6 | 67961 | 2 |
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 | 2.3 | 2.42 | 86.7 | 0.24 | 0.237 | 3.1 | 3.9 |
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 3NV8 | 2.3 | 44.02 | 64572 | 3380 | 96.94 | 0.14046 | 0.13923 | 0.16375 | RANDOM | 29.829 |
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] | |
-4.42 | -4.42 | 8.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.868 |
r_dihedral_angle_4_deg | 20.469 |
r_dihedral_angle_3_deg | 15.267 |
r_dihedral_angle_1_deg | 6.5 |
r_angle_refined_deg | 2.058 |
r_angle_other_deg | 0.942 |
r_chiral_restr | 0.119 |
r_bond_refined_d | 0.021 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7072 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms | 93 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |