2I5N
1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DXR | PDB ENTRY 1DXR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | THE CRYSTALS WERE GROWN BY MICROFLUIDIC TECHNIQUE USING CRYSTALLIZATION BUFFER: 1.6 - 1.8 M (NH4)2SO4 IN TRIS PH 7.8. THE ADDITIVES WERE HEPTANETRIOL (3%, W/V) AND 2% TRIETHYL AMONIUM PHOSPHATE. THE DETERGENT WAS LAURYL DIMETHYLAMINE-N-OXIDE (LDA). THE PROTEIN COMPLEX WAS IN SODIUM PHOSPHATE BUFFER PH 6.0 AND 0.08% LDA. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5 | 70 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 220.4 | α = 90 |
b = 220.4 | β = 90 |
c = 113.009 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | CCD | MARMOSAIC 300 mm CCD | ADJUSTABLE FOCUSING MIRRORS | 2006-07-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.96 | 20 | 94.5 | 0.082 | 17.5 | 5.9 | 189189 | 24.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.96 | 2 | 67.4 | 0.48 | 2.3 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1DXR | 1.96 | 20 | 189189 | 189189 | 9533 | 96.5 | 0.173 | 0.172 | 0.19 | RANDOM | 25.42 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.35 | 0.35 | -0.7 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.902 |
r_dihedral_angle_4_deg | 16.534 |
r_dihedral_angle_3_deg | 12.261 |
r_dihedral_angle_1_deg | 5.683 |
r_scangle_it | 3.506 |
r_scbond_it | 2.507 |
r_mcangle_it | 1.659 |
r_angle_refined_deg | 1.329 |
r_mcbond_it | 1.117 |
r_angle_other_deg | 1.055 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9282 |
Nucleic Acid Atoms | |
Solvent Atoms | 771 |
Heterogen Atoms | 970 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |