5HOZ
Crystal structure of Equine Serum Albumin (ESA) at pH 9.0
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5DQF |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 289 | 1 ul of 32 mg/ml protein in 10 mM Tris pH 7.5, 150 mM NaCl was mixed with 1 ul of the well condition (100 mM Tris, 2.4 M Ammonium phosphate, final pH 9.0) and equilibrated against well solution on 15-well Crystallization Plate (Qiagen) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 54.96 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.825 | α = 90 |
b = 93.825 | β = 90 |
c = 141.348 | 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 | MARMOSAIC 300 mm CCD | Beryllium Lenses | 2015-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.979 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.15 | 80.01 | 98.1 | 0.05 | 0.05 | 10.6 | 5.1 | 37617 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.15 | 2.19 | 94.3 | 0.737 | 1.8 | 4.7 |
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 | FREE R-VALUE | 5DQF | 2.15 | 80.01 | 35855 | 1761 | 98.19 | 0.1975 | 0.1955 | 0.2388 | RANDOM | 66.867 |
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] | |
1.69 | 0.85 | 1.69 | -5.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.776 |
r_dihedral_angle_4_deg | 20.021 |
r_dihedral_angle_3_deg | 13.557 |
r_mcangle_it | 7.118 |
r_mcbond_other | 5.816 |
r_mcbond_it | 5.814 |
r_dihedral_angle_1_deg | 5.045 |
r_angle_refined_deg | 1.458 |
r_angle_other_deg | 0.969 |
r_chiral_restr | 0.075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4407 |
Nucleic Acid Atoms | |
Solvent Atoms | 299 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | phasing |
Coot | model building |
MOLREP | phasing |
HKL-3000 | data reduction |
MD2 | data collection |