6IBJ
Copper binding protein from Laetisaria arvalis (LaX325)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 20 mM L-Na-Glutamate, 20 mM DL-Alanine (racemic), 20 mM Glycine, 20 mM DL-Lysine HCl (racemic), 20 mM DL-Serine (racemic) 100 mM MES monohydrate pH 6.5 / 100 mM imidazole pH 6.5 20% (w/v) PEG 500 MME and 10% (w/v) PEG 20.000. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.92 | α = 90 |
b = 74.92 | β = 90 |
c = 64.39 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 16M | Kirkpatrick-Baez (KB) mirror pair (VFM, HFM) | 2018-04-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.9799 | MAX IV | BioMAX |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.1 | 60 | 99.9 | 0.087 | 0.999 | 12.25 | 7.2 | 11173 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.1 | 2.15 | 99.9 | 0.1703 | 0.803 | 1.49 | 7.44 |
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 | 6IBI | 2.1 | 48.88 | 10600 | 575 | 99.85 | 0.19647 | 0.19351 | 0.25618 | RANDOM | 54.919 |
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] | |
2.2 | 2.2 | -4.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.247 |
r_dihedral_angle_4_deg | 12.578 |
r_dihedral_angle_3_deg | 12.387 |
r_long_range_B_other | 8.203 |
r_long_range_B_refined | 8.201 |
r_dihedral_angle_1_deg | 7.232 |
r_scangle_other | 6.714 |
r_mcangle_it | 5.304 |
r_mcangle_other | 5.302 |
r_scbond_it | 4.654 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1125 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |