5TJR
X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZZ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 281 | Protein at 5 mg/mL with added acetyl-CoA; crystal conditions were 100 mM bis-tris propane at pH 7.6, 24% PEG 3350, 210 mM trisodium citr ate in 150 plus 150 nL drops. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 115.891 | α = 90 |
b = 156.631 | β = 90 |
c = 192.246 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 315 | 2015-09-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.95 | 49.6 | 99.9 | 0.178 | 0.998 | 11.5 | 14.7 | 74332 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.95 | 3.01 | 100 | 1.607 | 0.818 | 2 | 15 |
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 | 4zz7 | 2.95 | 49 | 70516 | 3714 | 99.86 | 0.21417 | 0.21236 | 0.24862 | RANDOM | 72.029 |
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] | |
-4.13 | 7.93 | -3.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.035 |
r_dihedral_angle_4_deg | 19.73 |
r_dihedral_angle_3_deg | 17.191 |
r_long_range_B_refined | 14.274 |
r_long_range_B_other | 14.274 |
r_scangle_other | 8.656 |
r_mcangle_other | 8.043 |
r_mcangle_it | 8.042 |
r_dihedral_angle_1_deg | 5.984 |
r_scbond_it | 5.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 20813 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms | 135 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |