3TYI
Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1YCC | PDB ENTRY 1YCC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.3 | 293.15 | 26 % PEG 8000, 100 mM Magnesium Chloride, 50 mM Sodium Chloride, 50 mM Sodium Cacodylate pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.044 | α = 90 |
b = 55.317 | β = 90 |
c = 117.419 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 198.5 | CCD | MARMOSAIC 225 mm CCD | 2011-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 1.13 | ESRF | BM14 |
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 | 1.399 | 50 | 98.7 | 0.044 | 0.044 | 36.811 | 4.3 | 47273 | 47273 | -3 | 14.3 |
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 | 1.399 | 1.42 | 90.6 | 0.299 | 0.299 | 2.373 | 2.3 | 2082 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | 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 | PDB ENTRY 1YCC | 1.399 | 30.19 | 45566 | 954 | 98.43 | 0.17742 | 0.17696 | 0.19848 | RANDOM | 17.163 |
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] | |
-0.01 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.133 |
r_dihedral_angle_4_deg | 17.532 |
r_dihedral_angle_3_deg | 13.652 |
r_dihedral_angle_1_deg | 5.779 |
r_scangle_it | 2.967 |
r_scbond_it | 1.977 |
r_mcangle_it | 1.309 |
r_angle_refined_deg | 1.238 |
r_mcbond_it | 0.686 |
r_chiral_restr | 0.287 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1688 |
Nucleic Acid Atoms | |
Solvent Atoms | 388 |
Heterogen Atoms | 230 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALA | data scaling |