6SBI
X-ray structure of murine Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 291 | 20% PEG 4000, 0.05M MgCl2, 0.1M MES pH5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.603 | α = 90 |
b = 103.348 | β = 90.21 |
c = 86.597 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 2M | 2018-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.7 | 44.38 | 91.2 | 0.171 | 0.203 | 0.108 | 0.985 | 4.2 | 3.43 | 15791 | 38 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.71 | 2.97 | 51.4 | 0.543 | 0.648 | 0.351 | 0.757 | 1.4 | 3.32 |
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 | 6FOH | 2.7 | 44.37 | 15119 | 756 | 62.4 | 0.1893 | 0.1869 | 0.2344 | RANDOM | 31.973 |
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] | |
0.95 | 0.24 | -1.66 | 0.71 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.405 |
r_dihedral_angle_3_deg | 20.511 |
r_dihedral_angle_4_deg | 16.774 |
r_dihedral_angle_1_deg | 8.211 |
r_angle_refined_deg | 1.499 |
r_angle_other_deg | 1.182 |
r_chiral_restr | 0.06 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6704 |
Nucleic Acid Atoms | |
Solvent Atoms | 33 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
STARANISO | data scaling |
MOLREP | phasing |