4I25
2.00 Angstroms X-ray crystal structure of NAD- and substrate-bound 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2D4E | PDB entry 2D4E |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9.1 | 291 | 0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350 , pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 51.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.253 | α = 90 |
b = 142.932 | β = 90 |
c = 175.125 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2012-07-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.8 | APS | 22-ID |
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 | 35 | 100 | 0.12 | 34 | 14.4 | 149047 | 149047 | 26.67 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2 | 2.03 | 100 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 2D4E | 2 | 27.22 | 147418 | 7401 | 98.6 | 0.1645 | 0.1622 | 0.2081 | RANDOM | 29.3828 |
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] | |
-0.52 | -0.87 | 1.39 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_2_deg | 35.61 |
f_dihedral_angle_4_deg | 20.388 |
f_dihedral_angle_3_deg | 13.558 |
f_dihedral_angle_1_deg | 6.162 |
f_angle_refined_deg | 1.81 |
f_angle_other_deg | 0.917 |
f_chiral_restr | 0.118 |
f_bond_refined_d | 0.019 |
f_gen_planes_refined | 0.009 |
f_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14684 |
Nucleic Acid Atoms | |
Solvent Atoms | 1397 |
Heterogen Atoms | 220 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
SERGUI | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |