5ID9
Crystal structure of equine serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cPA)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4OT2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | 293 | 1.8 M Ammonium sulfate, 0.1 M acetate buffer pH 4.5, cocrystallization |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.23 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 93.86 | ¦Á = 90 |
b = 93.86 | ¦Â = 90 |
c = 141.79 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 |
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 | RAYONIX MX-225 | 2013-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9184 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.48 | 50 | 99.6 | 0.088 | 0.998 | 14.5 | 4.6 | 24973 | -3 | 53.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.48 | 2.58 | 99.4 | 0.991 | 2.1 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 4OT2 | 2.48 | 50 | 23957 | 1012 | 99.6 | 0.17261 | 0.17031 | 0.22906 | RANDOM | 55.701 |
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] | |
0.6 | 0.3 | 0.6 | -1.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.65 |
r_dihedral_angle_3_deg | 18.395 |
r_dihedral_angle_4_deg | 17.671 |
r_long_range_B_refined | 8.1 |
r_long_range_B_other | 8.096 |
r_dihedral_angle_1_deg | 6.402 |
r_scangle_other | 4.929 |
r_mcangle_it | 3.719 |
r_mcangle_other | 3.719 |
r_scbond_it | 2.999 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4568 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | phasing |
XDS | data reduction |
XSCALE | data scaling |