4YE1
A cytochrome c plus calixarene structure - alternative ligand binding mode
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3TYI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293.15 | 18 % PEG 8000, 50 mM NaCl, 100 mM MgCl2, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 35.85 | α = 90 |
b = 56.07 | β = 90 |
c = 108.04 | 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2011-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | 0.872600 | ESRF | ID23-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (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 | ||||||
1 | 1.392 | 108 | 100 | 0.088 | 0.095 | 0.035 | 14.6 | 7.2 | 44554 | 44554 |
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) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.39 | 1.47 | 100 | 0.418 | 0.418 | 0.168 | 1.8 | 7.1 | 6395 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3TYI | 1.39 | 26.38 | 42297 | 2245 | 99.97 | 0.1318 | 0.1303 | 0.1597 | RANDOM | 10.634 |
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] | |
-0.44 | -0.14 | 0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 30.968 |
r_dihedral_angle_2_deg | 30.745 |
r_dihedral_angle_4_deg | 28.47 |
r_sphericity_bonded | 17.854 |
r_rigid_bond_restr | 14.319 |
r_dihedral_angle_3_deg | 12.073 |
r_dihedral_angle_1_deg | 6.185 |
r_angle_refined_deg | 1.319 |
r_angle_other_deg | 1.16 |
r_mcangle_it | 0.921 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1690 |
Nucleic Acid Atoms | |
Solvent Atoms | 422 |
Heterogen Atoms | 236 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |