Joint Neutron and X-ray structure of Cytochrome c peroxidase
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | MICRODIALYSIS | 6 | 298 | 50mM potassium phosphate, 30% MPD, pH 6.0(in D2O), MICRODIALYSIS, temperature 298K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.16 | 61.08 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 51.547 | α = 90 |
b = 76.655 | β = 90 |
c = 107.078 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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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 | 298 | IMAGE PLATE | | | 2009-06-23 | M | LAUE |
2 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU RAXIS IV | | 2009-04-13 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 3.2-4.2 | ILL | LADI III |
2 | ROTATING ANODE | RIGAKU | 1.5418 | | |
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 | 2.4 | 53.55 | 76.3 | 0.168 | | | | | | 7.8 | 4.6 | 16906 | 12900 | | | 29.96 |
2 | 2.1 | 43.893 | 89.9 | | | | | | | | | | 22900 | | | |
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 | 2.4 | 2.53 | | 0.194 | | | | | | 5 | 2.5 | 1358 |
2 | 2.1 | 2.17 | | | | | | | | | | |
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 | 2.4 | 53.539 | | | | 12900 | 1290 | 75.01 | | 0.2115 | 0.2071 | 0.2499 | | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.1 | 43.893 | | 1.36 | | 22900 | 2292 | 89.89 | | 0.1698 | 0.1662 | 0.2027 | | 32.4685 |
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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-5.956 | | | -1.5485 | | -11.8662 |
1.3301 | | | 5.3682 | | -9.8548 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 19.996 |
f_angle_d | 1.649 |
f_chiral_restr | 0.173 |
f_bond_d | 0.016 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2367 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 43 |
Software
Software |
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Software Name | Purpose |
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QLD | data collection |
PHENIX | model building |
PHENIX | refinement |
LAUEGEN | data reduction |
SCALA | data scaling |
PHENIX | phasing |