8EW4
Human Serum Albumin with Cobalt (II) and Myristic Acid - crystal 1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6WUW | PDB entry 6WUW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.4 | 291.15 | 200 nL 22.5% PEG Smear Low, 10% isopropanol, 100 mM Tris, pH 7.4 + 200 nL 88 mg/mL albumin, saturated myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. 400 nL 45% PEG Smear Low, 20 mM cobalt chloride added 6 hours prior to harvesting. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 172.775 | α = 90 |
b = 38.503 | β = 103.55 |
c = 95.865 | 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 | 100 | PIXEL | DECTRIS EIGER X 9M | Mirrors | 2022-06-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.60394 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.4 | 40 | 97.2 | 0.053 | 0.063 | 0.034 | 14.1 | 3.3 | 24101 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.4 | 2.44 | 93.5 | 0.277 | 0.33 | 0.177 | 0.955 | 3.2 |
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 6WUW | 2.4 | 37.56 | 21539 | 1118 | 92.24 | 0.2061 | 0.2032 | 0.2621 | RANDOM | 40.738 |
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] | |
-2.07 | -0.57 | 0.03 | 2.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 14.198 |
r_dihedral_angle_1_deg | 5.675 |
r_dihedral_angle_2_deg | 4.46 |
r_angle_refined_deg | 0.891 |
r_angle_other_deg | 0.307 |
r_chiral_restr | 0.049 |
r_bond_refined_d | 0.003 |
r_gen_planes_refined | 0.003 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4643 |
Nucleic Acid Atoms | |
Solvent Atoms | 161 |
Heterogen Atoms | 164 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |
HKL-3000 | phasing |
PDB_EXTRACT | data extraction |