5LTI
Crystal structure of the alpha subunit of heme dependent oxidative N-demethylase (HODM) in complex with the dimethylamine substrate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LTE |
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 |
2.9 | 57.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.212 | α = 90 |
b = 80.212 | β = 90 |
c = 144.608 | 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 PILATUS 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 | 1.9 | 28.36 | 100 | 0.057 | 13.7 | 12 | 36266 |
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 | 1.9 | 2.01 | 100 | 0.306 | 4.5 | 12 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 5LTE | 1.9 | 28.36 | 36235 | 1909 | 99.94 | 0.17424 | 0.17283 | 0.20101 | RANDOM | 19.824 |
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] | |
-0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.643 |
r_dihedral_angle_4_deg | 19.982 |
r_dihedral_angle_3_deg | 14.308 |
r_dihedral_angle_1_deg | 6.422 |
r_angle_refined_deg | 2.113 |
r_angle_other_deg | 0.961 |
r_chiral_restr | 0.14 |
r_bond_refined_d | 0.025 |
r_gen_planes_refined | 0.014 |
r_gen_planes_other | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2738 |
Nucleic Acid Atoms | |
Solvent Atoms | 193 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
Coot | model building |