5EC6
The apo crystal structure of haemoglobin receptor HpuA from Kingella denitrificans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.8 | 277 | 100 mM imidazole, 150 mM lithium sulfate, 6% Peg 3000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.97 | 58.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.47 | α = 90 |
b = 102.47 | β = 90 |
c = 77.21 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 2014-08-02 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Cobalt SAD | 2014-08-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.008 | Diamond | I04 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.605 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.6 | 72.457 | 100 | 0.102 | 0.107 | 0.032 | 12.6 | 11.4 | 54716 | 54716 |
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) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.6 | 1.69 | 100 | 0.853 | 0.853 | 0.262 | 2.8 | 11.4 | 7872 |
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 | SAD | THROUGHOUT | 1.6 | 72.457 | 51939 | 2686 | 99.92 | 0.1719 | 0.1706 | 0.196 | RANDOM | 25.184 |
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] | |
0.81 | 0.81 | -1.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_mcangle_it | 3.014 |
r_mcbond_it | 1.947 |
r_mcbond_other | 1.939 |
r_angle_refined_deg | 1.608 |
r_angle_other_deg | 0.811 |
r_chiral_restr | 0.097 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2229 |
Nucleic Acid Atoms | |
Solvent Atoms | 325 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
autoSHARP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SCALA | data scaling |