7MBL
Crystal structure of Equine Serum Albumin in complex with Cobalt (II)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5IIU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | COUNTER-DIFFUSION | 7.4 | 291 | Protein: 1 uL of 34 mg/mL ESA dissolved in 10 mM Tris (pH 7.4) and 150 mM NaCl. Precipitant: 1 uL of 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M Tris pH 7.4. 15-Well hanging drop crystallization plate (Qiagen, EasyXtal). 3.3 uL of 50 mM cobalt (II) chloride dissolved in the reservoir solution were added directly to the 2 uL crystallization drop containing crystals to reach a final cobalt concentration of 31 mM and then incubated for a few hours before harvesting. Paratone was used as a cryoprotectant |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.7 | 54.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.312 | α = 90 |
b = 93.312 | β = 90 |
c = 141.51 | γ = 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 | ADSC QUANTUM 315r | 2017-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97929 | APS | 19-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.7 | 50 | 99.9 | 0.089 | 0.089 | 0.099 | 0.044 | 0.991 | 7.1 | 5 | 19239 | -3 | 54.2 |
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) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.7 | 2.75 | 100 | 1.124 | 1.124 | 1.256 | 0.557 | 0.751 | 1.3 | 5.1 |
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 | 5IIU | 2.7 | 46.7 | 16913 | 928 | 92.88 | 0.2174 | 0.2133 | 0.2892 | RANDOM | 58.041 |
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] | |
-0.23 | -0.11 | -0.23 | 0.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.027 |
r_dihedral_angle_3_deg | 17.26 |
r_dihedral_angle_4_deg | 16.911 |
r_dihedral_angle_1_deg | 5.947 |
r_angle_refined_deg | 1.342 |
r_angle_other_deg | 1.15 |
r_chiral_restr | 0.058 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4582 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | phasing |
HKL-3000 | data collection |
MOLREP | phasing |