Joint Xray/neutron crystal structure determination of fully perdeuterated rubredoxin at 295K
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 1BRF | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | hanging drop | | | 3.8 M sodium/potassium phosphate, hanging drop |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.31 | 46.86 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 34.374 | α = 90 |
b = 35.339 | β = 90 |
c = 44.111 | 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 | x-ray | 295 | IMAGE PLATE | MAR345 | | | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 295 | IMAGE PLATE | MAATEL LADI-III | | 2008-05-07 | L | LAUE |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | ROTATING ANODE | | 1.54 | | |
2 | NUCLEAR REACTOR | | 3.3-4.2 | | |
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 | 1.675 | 27.116 | 82.3 | 0.095 | 0.095 | | | | | 14.9 | 6.1 | | 6814 | | | |
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 | 1.675 | 1.77 | | 0.099 | 0.099 | | | | | 7 | 1.4 | 304 |
1 | 1.77 | 1.87 | | 0.101 | 0.101 | | | | | 6.7 | 2.9 | 622 |
1 | 1.87 | 2 | | 0.098 | 0.098 | | | | | 6.8 | 5.7 | 706 |
1 | 2 | 2.16 | | 0.1 | 0.1 | | | | | 6.4 | 7.7 | 701 |
1 | 2.16 | 2.37 | | 0.102 | 0.102 | | | | | 5.8 | 7.9 | 673 |
1 | 2.37 | 2.65 | | 0.099 | 0.099 | | | | | 6.1 | 7 | 629 |
1 | 2.65 | 3.06 | | 0.096 | 0.096 | | | | | 5.8 | 6.5 | 559 |
1 | 3.06 | 3.75 | | 0.093 | 0.093 | | | | | 6.3 | 6.5 | 494 |
1 | 3.75 | 5.3 | | 0.092 | 0.092 | | | | | 5.8 | 7.3 | 387 |
1 | 5.3 | 27.12 | | 0.067 | 0.067 | | | | | 6.9 | 5.4 | 236 |
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 | 1.675 | 12.627 | | 1.56 | | 5311 | 305 | 91.1 | | 0.17 | 0.169 | 0.197 | | 21.155 |
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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-1.851 | | | -6.575 | | -5.814 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 19.981 |
f_angle_d | 0.969 |
f_chiral_restr | 0.072 |
f_bond_d | 0.005 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 403 |
Nucleic Acid Atoms | |
Solvent Atoms | 28 |
Heterogen Atoms | 1 |
Software
Software |
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Software Name | Purpose |
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SCALA | data processing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
LAUEGEN | data reduction |
SCALA | data scaling |