4U9K
Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II)NO ligation state, Q154A/Q155A/K156A mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 293 | OBTAINED BY EQUILIBRATING A 2 UL DROP OF 1:1 PROTEIN:RESERVOIR AGAINST A 700 UL RESERVOIR CONTAINING 1.6-1.9 M DL-MALIC ACID (PH 7.3). FOR CRYOPROTECTION, 2 UL OF MOTHER LIQUOR CONTAINING 10% GLYCEROL WAS ADDED DIRECTLY TO THE DROP AND CRYSTALS WERE SERIAL TRANSFERRED INTO MOTHER LIQUOR SOLUTION CONTAINING 5, 7.5 AND 10% GLYCEROL. PRIOR TO FLASH FREEZING IN LIQUID NITROGEN, CRYSTALS WERE TRANSFERRED UNDER A LAYER OF OIL AND INCUBATED WITH ANAEROBIC CRYOPROTECTANT CONTAINING APPROXIMATELY 0.001 M NITRIC OXIDE FOR 15-45 MINUTES. CRYSTAL GROWTH AND MANIPULATION WAS PERFORMED ANAEROBICALLY. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.57 | 73.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 164.303 | α = 90 |
b = 164.303 | β = 90 |
c = 101.679 | γ = 120 |
Symmetry | |
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Space Group | P 63 2 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 | CCD | ADSC QUANTUM 315r | 2013-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.00 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.45 | 47.875 | 99.77 | 0.032 | 19.3 | 10.7 | 56342 | 56342 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.45 | 2.55 | 100 | 0.663 | 1.6 | 11 |
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 | 4U9J | 2.45 | 47.875 | 1.34 | 56342 | 2848 | 99.77 | 0.1835 | 0.1822 | 0.2069 |
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 | 14.738 |
f_angle_d | 1.643 |
f_chiral_restr | 0.176 |
f_bond_d | 0.022 |
f_plane_restr | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2951 |
Nucleic Acid Atoms | |
Solvent Atoms | 47 |
Heterogen Atoms | 91 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |