Joint Xray/neutron crystal structure determination of H-labeled 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 | | | | 3.8 M sodium/potassium phosphate, hanging drop |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.2 | 44.1 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 34.238 | α = 90 |
b = 35.096 | β = 90 |
c = 43.858 | 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 | CCD | MARMOSAIC 225 mm CCD | | 2008-03-09 | | SINGLE WAVELENGTH |
2 | 1 | neutron | 295 | IMAGE PLATE | MAATEL LADI-III | | | | LAUE |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | APS BEAMLINE 22-BM | | APS | 22-BM |
2 | NUCLEAR REACTOR | | | | |
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 | 1.1 | 27.4 | | | | | | | | | | | 21725 | | | |
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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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.1 | 24.51 | | 1.35 | | 21691 | 1107 | 98.2 | | 0.145 | 0.145 | 0.156 | | 16.79 |
NEUTRON DIFFRACTION | | 1.66 | 27.4 | | 1.09 | | 4602 | 209 | 69.7 | | 0.188 | 0.187 | 0.202 | | |
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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0.82 | | | 0.296 | | 0.425 |
-0.25 | | | 0.828 | | 1.536 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 18.003 |
f_angle_d | 1.426 |
f_chiral_restr | 0.095 |
f_bond_d | 0.014 |
f_plane_restr | 0.011 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 414 |
Nucleic Acid Atoms | |
Solvent Atoms | 37 |
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 |