5UTC
Deoxy form of sperm whale myoglobin V68A/I107Y
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 294 | 0.1 M Tris-HCl, 1 mM EDTA, pH 7.4 2.56 M Ammonium Sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.454 | α = 90 |
b = 30.565 | β = 105.58 |
c = 63.811 | 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 | PIXEL | DECTRIS PILATUS 200K | 2013-11-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.8 | 31 | 99 | 0.046 | 0.056 | 0.031 | 39.5 | 3 | 12004 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.8 | 1.83 | 94.3 | 0.07 | 0.089 | 0.054 | 0.986 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.8 | 26.37 | 11396 | 601 | 98.9 | 0.1887 | 0.1856 | 0.2504 | RANDOM | 23.633 |
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] | |
-0.34 | -0.41 | 0.96 | -0.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.092 |
r_dihedral_angle_4_deg | 23.637 |
r_dihedral_angle_3_deg | 14.795 |
r_dihedral_angle_1_deg | 5.166 |
r_angle_refined_deg | 1.875 |
r_angle_other_deg | 0.929 |
r_chiral_restr | 0.157 |
r_bond_refined_d | 0.018 |
r_gen_planes_refined | 0.011 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1214 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL | data scaling |