3WHN
Hemerythrin-like domain of DcrH I119H mutant (met)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3AGT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.2 | 283 | 30 % (W/V) PEG 4000, 0.2M CaCl2, 12% (V/V) isopropanol, 0.1M TrisHCl, pH 8.2, vapor diffusion, hanging drop, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 33.573 | α = 92.71 |
b = 44.082 | β = 102.59 |
c = 46.715 | γ = 90.02 |
Symmetry | |
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Space Group | P 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 | CCD | RAYONIX MX225HE | mirrors | 2013-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.00 | SPring-8 | BL41XU |
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 | 1.9 | 30 | 97.9 | 0.098 | 0.098 | 14.282 | 4 | 20052 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 1.97 | 96.4 | 0.323 | 0.323 | 4.167 | 4 |
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 | 3AGT | 1.9 | 20 | 20052 | 1013 | 97.7 | 0.1959 | 0.1933 | 0.2476 | RANDOM | 12.5531 |
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] | |
-0.23 | -0.23 | 0.01 | -0.82 | 0.01 | 0.94 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.551 |
r_dihedral_angle_4_deg | 17.765 |
r_dihedral_angle_3_deg | 14.563 |
r_dihedral_angle_1_deg | 5.118 |
r_angle_refined_deg | 1.356 |
r_chiral_restr | 0.099 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2250 |
Nucleic Acid Atoms | |
Solvent Atoms | 270 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SPACE | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |