1LS9
Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CTJ | PDB ENTRY 1CTJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.6 | 277 | 0.2 M Na-acetate, 0.1 M Na-cacodylate, pH 6.5, 30% w/v PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.063 | α = 90 |
b = 46.063 | β = 90 |
c = 100.526 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | 100 | IMAGE PLATE | MARRESEARCH | 165-mm MAR CCD | 2001-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X13 | 0.8015 | EMBL/DESY, HAMBURG | X13 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.3 | 14.8906 | 98.4 | 0.053 | 25.3 | 20.25 | 27067 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.3 | 1.32 | 97.6 | 0.311 | 3.6 | 38.68 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1CTJ | 1.3 | 14.684 | 25709 | 1358 | 98.6 | 0.157 | 0.14922 | 0.14339 | 0.19034 | RANDOM | 16.595 |
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] | |
0.4835 | 0.4835 | 0.0177 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 17.8 |
p_staggered_tor | 11.2 |
p_planar_tor | 5.3 |
p_scangle_it | 4.29 |
p_scbond_it | 3.384 |
p_mcangle_it | 2.8 |
p_mcbond_it | 2.405 |
p_multtor_nbd | 0.278 |
p_singtor_nbd | 0.165 |
p_chiral_restr | 0.138 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 674 |
Nucleic Acid Atoms | |
Solvent Atoms | 200 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |