5NQM
CU(I)-CSP3 (COPPER STORAGE PROTEIN 3) FROM METHYLOSINUS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5ARM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 200 mM MgCl2, 100 mM Hepes pH 7.5, 30% PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.87 | 34.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.65 | α = 90 |
b = 106.68 | β = 90 |
c = 45.62 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 PILATUS3 6M | 2015-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 1.3746 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.59 | 45.62 | 99.3 | 0.083 | 7.8 | 3.6 | 14862 |
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 | 1.59 | 1.62 | 99.3 | 0.382 | 3.3 |
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 | 5ARM | 1.59 | 45.62 | 14138 | 724 | 98.97 | 0.1527 | 0.15002 | 0.20655 | RANDOM | 20.412 |
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 | -0.65 | 0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.265 |
r_dihedral_angle_4_deg | 17.216 |
r_sphericity_free | 16.344 |
r_dihedral_angle_3_deg | 14.989 |
r_sphericity_bonded | 7.981 |
r_dihedral_angle_1_deg | 4.143 |
r_scangle_other | 3.703 |
r_long_range_B_other | 3.527 |
r_long_range_B_refined | 3.524 |
r_scbond_it | 3.461 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 935 |
Nucleic Acid Atoms | |
Solvent Atoms | 38 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
iMOSFLM | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |