7KRG
Crystal Structure of Mannitol Dehydrogenase (ChMDH) from Cladosporium herbarum in complex with NADP+ and Na
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 25% PEG 1500, 100 mM sodium propionate/sodium cacodylate/BIS-TRIS propane (2:1:2 molar ratio), pH 7, 5 mM NADP+ |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.867 | α = 90 |
b = 119.322 | β = 94.884 |
c = 111.211 | 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 | CCD | ADSC QUANTUM 315 | 2015-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.979 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | 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 | 2.0379 | 50 | 97.6 | 0.087 | 0.137 | 16.6 | 2.9 | 141106 | 27.8196736865 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.0379 | 2.09 | 0.656 |
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 | 3GDF | 2.03797368098 | 31.4045238396 | 1.3435622572 | 141045 | 1990 | 95.8485668076 | 0.154547684041 | 0.154135383197 | 0.182916664342 | 32.9031283964 |
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 | 4.93040445067 |
f_angle_d | 0.828817897269 |
f_chiral_restr | 0.0508401352847 |
f_bond_d | 0.00703664459293 |
f_plane_restr | 0.0041607803175 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15923 |
Nucleic Acid Atoms | |
Solvent Atoms | 1414 |
Heterogen Atoms | 388 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
SBC-Collect | data collection |
Coot | model building |
HKL-3000 | data scaling |
PHASER | phasing |
HKL-3000 | data reduction |