2HX8
Crystal structure of Cu(I) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM", at pH5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 29-31% PEG 4000, 100mM magnesium chloride, 100mM Sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.905 | α = 90 |
b = 65.345 | β = 90 |
c = 97.707 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 93 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic "blue" | 2006-03-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.542 |
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 | 1.547 | 54.317 | 99.8 | 0.053 | 0.053 | 10.2 | 6.7 | 33470 | 16.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.6 | 1.69 | 99 | 0.302 | 0.302 | 2.4 | 6.5 | 4783 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | Direct use of Oxidised structure in same crystal form | THROUGHOUT | Cu(II) form of the protein | 1.6 | 54.31 | 33411 | 1667 | 99.66 | 0.14 | 0.14 | 0.138 | 0.184 | RANDOM | 10.285 |
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] | |
-0.97 | 0.96 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.254 |
r_dihedral_angle_1_deg | 11.236 |
r_dihedral_angle_3_deg | 10.916 |
r_dihedral_angle_4_deg | 10.045 |
r_sphericity_free | 8.093 |
r_scangle_it | 3.945 |
r_sphericity_bonded | 3.336 |
r_scbond_it | 2.966 |
r_mcangle_it | 1.956 |
r_mcbond_it | 1.595 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1902 |
Nucleic Acid Atoms | |
Solvent Atoms | 448 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
MOSFLM | data reduction |
CCP4 | data scaling |