6TE3
Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.8 | 277 | 600 mM sodium formate, 12% PGA-LM, 100 mM HEPES/NaOH, 500 mM FeCl2, 500 mM MnCl2, 1 mM UDP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.31 | 62.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.995 | α = 90 |
b = 100.035 | β = 90 |
c = 225.208 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | PIXEL | DECTRIS EIGER X 4M | 2017-04-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.3 | 48.84 | 98.7 | 0.118 | 0.086 | 0.997 | 8.4 | 4.8 | 48288 | 26.46 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.3 | 2.38 | 99.7 | 1.476 | 1.107 | 0.512 | 0.9 | 4.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6FXM | 2.3 | 48.84 | 1.34 | 30657 | 1642 | 62.54 | 0.197 | 0.1943 | 0.2458 | 35.83 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.4936 |
f_angle_d | 0.6179 |
f_chiral_restr | 0.044 |
f_plane_restr | 0.0048 |
f_bond_d | 0.0036 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5611 |
Nucleic Acid Atoms | |
Solvent Atoms | 155 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
STARANISO | data scaling |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |