4R41
Complex Crystal structure of 4-nitro-2-phosphono-benzoic acid with sp-Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-dinucleotide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4R3N | PDB entry 4R3N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | 15-22% PEG 3350, 0.1 M Na-acetate, 0.1 M MES buffer (pH 6.5), 10mM TCEP, 3% Ethylene Glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.82 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 59.595 | ¦Á = 90 |
b = 97.733 | ¦Â = 102.52 |
c = 63.943 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 300 mm CCD | double crystal monochromator and K-B pair of biomorph mirrors | 2012-08-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.033 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.6 | 50 | 88.7 | 0.1 | 9.2 | 2.5 | 92850 | 82360 | 1 | 1 | 14.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.6 | 1.66 | 47.6 | 0.527 | 1 | 1.2 | 4387 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 4R3N | 1.61 | 50 | 1 | 88550 | 78218 | 4110 | 88.33 | 0.18926 | 0.18793 | 0.21463 | RANDOM | 20.977 |
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] | |
0.62 | -0.28 | 0.92 | -1.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.263 |
r_dihedral_angle_4_deg | 18.87 |
r_dihedral_angle_3_deg | 13.4 |
r_dihedral_angle_1_deg | 6.029 |
r_long_range_B_refined | 4.646 |
r_scbond_it | 1.831 |
r_mcangle_it | 1.755 |
r_angle_refined_deg | 1.4 |
r_mcbond_it | 1.104 |
r_chiral_restr | 0.09 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5366 |
Nucleic Acid Atoms | |
Solvent Atoms | 328 |
Heterogen Atoms | 167 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |