3DU0
E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | hanging drop | 10 | 277 | 1.8M K2HPO4, N-octyl-beta-(R)-glucopyranoside, pH 10, hanging drop, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.7 | 66.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.95 | α = 90 |
b = 120.95 | β = 90 |
c = 110.03 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | IMAGE PLATE | RIGAKU RAXIS IV | OSMIC BLUE MIRRORS | 2005-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
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 | 32.14 | 99.6 | 0.083 | 10.4 | 4.08 | 62822 | 3 | 25.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2 | 32.14 | 62813 | 3143 | 99.61 | 0.191 | 0.188 | 0.245 | RANDOM | 27.838 |
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 |
r_dihedral_angle_2_deg | 38.514 |
r_dihedral_angle_4_deg | 17.64 |
r_dihedral_angle_3_deg | 16.054 |
r_dihedral_angle_1_deg | 7.562 |
r_scangle_it | 4.769 |
r_scbond_it | 3.37 |
r_mcangle_it | 1.888 |
r_angle_refined_deg | 1.221 |
r_mcbond_it | 1.156 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4390 |
Nucleic Acid Atoms | |
Solvent Atoms | 522 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |