Neutron crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXalpha at room temperature.
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 5.9 | 293 | Ammonium Sulfate, NaCl, MES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.65 | 53.61 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 71.107 | α = 90 |
b = 97.278 | β = 90 |
c = 43.174 | γ = 90 |
Symmetry |
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Space Group | P 21 21 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | neutron | 273 | | | WLS-fiber-based scintillator detector | 2013-04-10 | M | LAUE |
2 | 1 | x-ray | 273 | CCD | ADSC QUANTUM 270 | | 2013-11-05 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | NUCLEAR REACTOR | J-PARC MLF BEAMLINE BL-03 | 3.0-5.6 | JPARC MLF | BL-03 |
2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0 | Photon Factory | AR-NE3A |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (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 |
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1 | 1.55 | 50 | 99.4 | | | | | | | | | 44240 | 43975 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.55 | 1.58 | | | | | | | | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution 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 |
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NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.932 | 21.189 | | | 18379 | 18379 | 1839 | 79.39 | | 0.1731 | 0.1671 | 0.2271 | | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.551 | 36.904 | | 1.34 | 44184 | 43919 | 3829 | 99.38 | | 0.1451 | 0.1431 | 0.1654 | | |
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] |
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| | | | | |
| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 23.76 |
f_angle_d | 1.376 |
f_chiral_restr | 0.06 |
f_bond_d | 0.011 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1931 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 44 |
Software
Software |
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Software Name | Purpose |
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ADSC | data collection |
CNS | refinement |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |