6H1S
Structure of the BM3 heme domain in complex with fluconazole
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KF2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | PEG, 5mM ligand (dissolved in 100% DMSO), 25mM potassium phosphate pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.66 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 60.937 | ¦Á = 90 |
b = 119.291 | ¦Â = 90 |
c = 146.494 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 PILATUS3 S 6M | 2017-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.98 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 1.95 | 119.29 | 100 | 0.113 | 1 | 10.7 | 6.6 | 74443 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.95 | 1.99 | 100 | 0.815 | 0.8 | 6.1 |
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 | 4KF2 | 1.95 | 73.35 | 74443 | 3825 | 99.87 | 0.17671 | 0.17479 | 0.21364 | RANDOM | 36.523 |
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] | |
-1.28 | 1.03 | 0.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.149 |
r_dihedral_angle_4_deg | 16.37 |
r_dihedral_angle_3_deg | 14.257 |
r_dihedral_angle_1_deg | 6.539 |
r_angle_refined_deg | 1.958 |
r_angle_other_deg | 1.282 |
r_chiral_restr | 0.119 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.011 |
r_gen_planes_other | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7211 |
Nucleic Acid Atoms | |
Solvent Atoms | 561 |
Heterogen Atoms | 191 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |