6EYE
Crystal structure of murine neuroglobin under 150 bar krypton
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4O4T |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | 1.6M AMMONIUM SULPHATE, 0.1M MES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.854 | α = 90 |
b = 87.854 | β = 90 |
c = 113.21 | γ = 120 |
Symmetry | |
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Space Group | H 3 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-F | 2016-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.8556 | ESRF | ID30B |
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) | 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 | 1.7 | 45.41 | 99.8 | 0.043 | 0.045 | 0.013 | 0.999 | 28.3 | 19.6 | 18730 | 2 | 4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.7 | 1.8 | 99.1 | 0.275 | 0.318 | 0.151 | 0.893 | 4.7 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 4O4T | 1.7 | 45.41 | 17859 | 866 | 99.81 | 0.1962 | 0.19373 | 0.25394 | RANDOM | 40.372 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.592 |
r_dihedral_angle_4_deg | 20.945 |
r_dihedral_angle_3_deg | 16.139 |
r_long_range_B_refined | 9.283 |
r_long_range_B_other | 9.255 |
r_scangle_other | 7.049 |
r_dihedral_angle_1_deg | 5.659 |
r_mcangle_it | 5.279 |
r_mcangle_other | 5.276 |
r_scbond_it | 4.656 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1172 |
Nucleic Acid Atoms | |
Solvent Atoms | 81 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
REFMAC | phasing |