5LTE
Crystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | The HODM-heme subunit was crystallised at 3 mg ml-1 in 50 mM KPi, 100 mM KCl, pH 7.5. Initial crystallisation conditions were identified using the JCSG+ matrix screen (Molecular dimensions). Crystals suitable for diffraction experiments were obtained by sitting drop vapour diffusion at 277 K in 400 nL drops containing equal volumes of protein and a solution containing 30% PEG 2K MME and 0.1 M potassium thiocyanate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.908 | α = 90 |
b = 79.908 | β = 90 |
c = 144.712 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | 100 | PIXEL | DECTRIS PILATUS3 X 2M | 2012-04-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.917 | Diamond | I04-1 |
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 | 1.65 | 26.82 | 99.93 | 0.061 | 15.4 | 12.1 | 53715 |
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 | 1.65 | 1.7 | 100 | 0.783 | 3.8 | 12.2 |
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 | MIR | THROUGHOUT | 1.65 | 26.82 | 53715 | 2872 | 99.93 | 0.16493 | 0.16341 | 0.19359 | RANDOM | 15.861 |
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 | 31.968 |
r_dihedral_angle_4_deg | 19.258 |
r_dihedral_angle_3_deg | 12.778 |
r_dihedral_angle_1_deg | 6.549 |
r_angle_refined_deg | 2.23 |
r_angle_other_deg | 1.017 |
r_chiral_restr | 0.158 |
r_bond_refined_d | 0.024 |
r_gen_planes_refined | 0.014 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2733 |
Nucleic Acid Atoms | |
Solvent Atoms | 321 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MLPHARE | phasing |