6HG8
Crystal structure of the R460G disease-causing mutant of the human dihydrolipoamide dehydrogenase.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.9 | 293.15 | protein in: 100 mM Tris,150 mM NaCl, 1 mM EDTA, pH 8.0 reservoir solution: 2 M (NH4)2SO4, 2 v/v% PEG-400, 0.1 M HEPES (pH 6.9) volume ratio: 1 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.92 | 57.87 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 117.913 | α = 90 |
b = 169.497 | β = 90 |
c = 61.401 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2017-08-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.76 | 48.4 | 93 | 0.141 | 0.998 | 9.5 | 6.8 | 114691 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.76 | 1.86 | 71.2 | 0.255 | 0.365 | 0.59 | 6.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1ZMD | 1.76 | 30 | 111625 | 2083 | 92.19 | 0.1883 | 0.18737 | 0.2374 | RANDOM | 33.417 |
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] | |
0.87 | -2.95 | 2.08 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.678 |
r_dihedral_angle_3_deg | 15.39 |
r_dihedral_angle_4_deg | 11.847 |
r_long_range_B_refined | 7.407 |
r_long_range_B_other | 7.406 |
r_dihedral_angle_1_deg | 6.636 |
r_scangle_other | 5.779 |
r_scbond_it | 3.927 |
r_scbond_other | 3.926 |
r_mcangle_it | 3.457 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7072 |
Nucleic Acid Atoms | |
Solvent Atoms | 904 |
Heterogen Atoms | 169 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MxCuBE | data collection |
XDS | data scaling |
XDS | data reduction |
MOLREP | phasing |