3QQX
Reduced Native Intermediate of the Multicopper Oxidase CueO
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KV7 | PDB entry 1KV7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 16% POLYETHYLENE GLYCOL 4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.173 | α = 90 |
b = 91.375 | β = 102.22 |
c = 54.328 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | IMAGE PLATE | RIGAKU RAXIS IV++ | Osmic Confocal Blue | 2007-03-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 1.5 | 53.07 | 96 | 0.055 | 9.8 | 2.3 | 73797 | 73797 |
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 | 1.5 | 1.55 | 93 | 0.338 | 2.2 | 1.9 | 7106 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | THROUGHOUT | PDB entry 1KV7 | 1.5 | 24.35 | 73702 | 69981 | 3721 | 96.4 | 0.20774 | 0.2059 | 0.24226 | RANDOM | 22.68 |
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] | |
-0.13 | -0.69 | -0.45 | 0.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.75 |
r_dihedral_angle_4_deg | 21.851 |
r_dihedral_angle_3_deg | 12.761 |
r_dihedral_angle_1_deg | 6.676 |
r_scangle_it | 3.573 |
r_scbond_it | 2.304 |
r_angle_refined_deg | 1.54 |
r_mcangle_it | 1.431 |
r_angle_other_deg | 0.919 |
r_mcbond_it | 0.845 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3640 |
Nucleic Acid Atoms | |
Solvent Atoms | 579 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
REFMAC | refinement |
CrystalClear | data reduction |
CrystalClear | data scaling |