6HR8
HMG-CoA reductase from Methanothermococcus thermolithotrophicus in complex with NADPH at 2.9 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6HR7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 291 | HMGR at 10 mg/ml was supplemented with a final concentration of 2 mM NADPH. The sample was centrifuged for 5 minute at 13.000 RPM to remove any aggregates and dust. 0.7 ul of protein sample was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) and 0.7 ul of reservoir solution was mixed. The best crystals were obtained after several month using a solution containing 40% v/v PEG 400, 100 mM Tris PH 8.5 and 200 mM Li2SO4. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 231.79 | α = 90 |
b = 231.79 | β = 90 |
c = 98.714 | γ = 90 |
Symmetry | |
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Space Group | P 4 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 6M | 2017-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | 0.97662 | ESRF | ID23-1 |
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 | 2.9 | 25 | 99.8 | 0.095 | 0.102 | 0.037 | 0.999 | 13.3 | 7.3 | 59867 | 93.25 |
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 | 2.9 | 3.06 | 100 | 1.285 | 1.377 | 0.491 | 0.427 | 1.6 | 7.7 |
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 | 6HR7 | 2.9 | 24.987 | 1.34 | 59830 | 2998 | 99.96 | 0.2127 | 0.2111 | 0.2426 | 113 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.28 |
f_angle_d | 0.653 |
f_chiral_restr | 0.047 |
f_bond_d | 0.003 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17794 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 279 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |