4US9
Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with 3- phenylpropionaldehyde
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VLB | PDB ENTRY 1VLB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 277 | VAPOR DIFFUSION, SITTING DROP, AT 277 K. CRYSTALLIZED USING 30% ISOPROPANOL, 0.2M MGCL2, 0.2M HEPES PH 7.6. ISOPROPANOL WAS REMOVED AND CRYSTAL WAS SOAKED WITH 1MM 3-PHENYLPROPIONALDEHYDE FOR 1H. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.3 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 143.766 | ¦Á = 90 |
b = 143.766 | ¦Â = 90 |
c = 162.544 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
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 | 77 | CCD | ADSC QUANTUM 315r | 2012-06-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | SOLEIL | PROXIMA 1 |
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 | 1.4 | 124.51 | 99.9 | 0.05 | 26.1 | 11.1 | 192977 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.4 | 1.42 | 97.4 | 0.19 | 9.8 | 10.6 |
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 1VLB | 1.4 | 124.51 | 183064 | 9694 | 99.8 | 0.09462 | 0.09343 | 0.11696 | RANDOM | 11.161 |
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] | |
0.02 | 0.01 | 0.02 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.278 |
r_sphericity_free | 34.658 |
r_dihedral_angle_4_deg | 16.536 |
r_dihedral_angle_3_deg | 11.496 |
r_sphericity_bonded | 8.34 |
r_dihedral_angle_1_deg | 6.808 |
r_rigid_bond_restr | 2.192 |
r_angle_refined_deg | 2.007 |
r_scbond_it | 1.258 |
r_mcangle_it | 1.173 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6815 |
Nucleic Acid Atoms | |
Solvent Atoms | 1360 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |