3HXJ
Crystal Structure of Pyrrolo-quinoline quinone (PQQ_DH) from Methanococcus maripaludis, Northeast Structural Genomics Consortium Target MrR86
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | microbatch, under oil | 5.5 | 291 | Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1 M Bis-Tris (pH 5.5), 25% PEG3350, and 0.2 M Lithium sulfate, microbatch, under oil, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.26 | 45.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.225 | α = 90 |
b = 66.958 | β = 115.29 |
c = 112.082 | 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 | MARMOSAIC 325 mm CCD | mirrors | 2009-05-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97905 | SSRL | BL9-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 30 | 98.7 | 0.067 | 0.058 | 17.5 | 3.6 | 176293 | 173972 | 7.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.07 | 89.2 | 0.281 | 0.241 | 3 | 2.4 | 17652 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2 | 19.98 | 2 | 2 | 176288 | 151608 | 7581 | 86 | 0.197 | 0.196 | 0.195 | 0.242 | RANDOM | 26.5 |
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] | |
-2.49 | -2.29 | 1.94 | 0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 26.6 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.76 |
c_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9498 |
Nucleic Acid Atoms | |
Solvent Atoms | 669 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
MAR345dtb | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
SnB | phasing |
REFMAC | refinement |