1HJ3
Cytochrome cd1 Nitrite Reductase, dioxygen complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1AOF | PDB ENTRY 1AOF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 293 | 2.3 M AMMONIUM SULFATE 50MM POTASSIUM PHOSPHATE PH 7.0 CRYSTALS WERE REDUCED USING 20MM SODIUM DITHIONITE. THE CRYSTAL WAS TRANSFERRED TO A SOLUTION CONTAINING 2.3 M AMMONIUM SULFATE, 50 MM PHOSPAHTE BUFFER PH 7 AND 15 % GLYCEROL. O2 WAS INTRODUCED UNDER 15 ATM PRESSURE FOR 2 MINUTES AT -20 DEGREES. THE DATA SET IS COMPOSED 10 DEGREE WEDGES OF DATA FROM 11 IDENTICAL CRYSTALS. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.19 | α = 90 |
b = 61.17 | β = 112.19 |
c = 100.52 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | MARRESEARCH | 1999-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.6 | 30 | 85.3 | 0.046 | 0.046 | 14.1 | 2.1 | 135637 | 17.714 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.6 | 1.66 | 85.4 | 0.175 | 0.175 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1AOF | 1.6 | 30 | 135637 | 85.3 | 0.196 | 0.219 | RANDOM |
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 |
p_transverse_tor | 29.4 |
p_special_tor | 15 |
p_staggered_tor | 11.2 |
p_planar_tor | 4.5 |
p_multtor_nbd | 0.241 |
p_singtor_nbd | 0.179 |
p_xyhbond_nbd | 0.149 |
p_chiral_restr | 0.127 |
p_plane_restr | 0.024 |
p_planar_d | 0.018 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8445 |
Nucleic Acid Atoms | |
Solvent Atoms | 795 |
Heterogen Atoms | 213 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |