4BKE
Recombinant human serum albumin with palmitic acid. Synthetic cationic antimicrobial peptides bind with their hydrophobic parts to drug site II of human serum albumin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E7H | PDB ENTRY 1E7H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.2 | 26 % PEG 3350, 50 MM KH2PO4 PH 7.2; 120 MG/ML IN 20 MM KH2PO4 AT PH 7.5 CONTAINING NOMINAL 0.1 MM PALMITIC ACID STREAK SEEDED SEEDING |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 189.366 | α = 90 |
b = 39.003 | β = 105.48 |
c = 96.296 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 295 | IMAGE PLATE | RIGAKU R-AXIS IV | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 2.35 | 38.14 | 96.5 | 0.07 | 9.3 | 5 | 27926 |
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 | 2.35 | 2.48 | 95.2 | 0.66 | 2.2 | 5 |
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 | PDB ENTRY 1E7H | 2.35 | 20 | 25867 | 2006 | 96.63 | 0.20167 | 0.1975 | 0.25434 | RANDOM | 56.95 |
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] | |
2.6 | 0.34 | -0.64 | -1.78 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.758 |
r_dihedral_angle_4_deg | 19.302 |
r_dihedral_angle_3_deg | 17.997 |
r_dihedral_angle_1_deg | 4.764 |
r_scangle_it | 2.496 |
r_scbond_it | 1.43 |
r_angle_refined_deg | 1.125 |
r_mcangle_it | 1.035 |
r_mcbond_it | 0.535 |
r_chiral_restr | 0.079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4630 |
Nucleic Acid Atoms | |
Solvent Atoms | 26 |
Heterogen Atoms | 119 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |