5OHF
Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide, partially reduced
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5OHE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 298 | 20.7% (w/v) PEG3350, 200 mM MgCl2, 0.01 M KCN, 7.5% (v/v) glycerol, 0.1 M MMT buffer system (DL-Malic acid, MES monohydrate, Tris, NaOH, HCl), pH 6.7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.685 | α = 90 |
b = 77.685 | β = 90 |
c = 441.238 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 PILATUS 6M | 2015-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 1.000 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 1.8 | 49.17 | 100 | 0.059 | 0.034 | 0.993 | 16.7 | 7.3 | 127077 | -3.7 | 21 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.8 | 1.83 | 100 | 0.761 | 0.442 | 0.844 | 2.7 | 7.6 |
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 | 5OHE | 1.8 | 49.17 | 126873 | 6224 | 99.98 | 0.19172 | 0.18991 | 0.23867 | Random selection | 28 |
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] | |
0.59 | 0.59 | -1.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.001 |
r_dihedral_angle_4_deg | 18.833 |
r_dihedral_angle_3_deg | 14.257 |
r_long_range_B_refined | 4.982 |
r_long_range_B_other | 4.832 |
r_dihedral_angle_1_deg | 4.32 |
r_scangle_other | 3.089 |
r_mcangle_it | 2.239 |
r_mcangle_other | 2.239 |
r_scbond_it | 1.89 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9821 |
Nucleic Acid Atoms | |
Solvent Atoms | 1016 |
Heterogen Atoms | 366 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |