8AD7
Flavin-dependent tryptophan 6-halogenase Thal in complex with D-Trp
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6H43 | 6H43 CHAINA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.2 | 293 | RESERVOIR: 0.1 M BICINE PH 8.2, 1.6 M K2HPO4/KH2PO4; PROTEIN CONCENTRATION: ~ 15 MG/ML; PROTEIN BUFFER: 10 MM TRIS PH 7.4, 50 MM NACL, 1 MM TCEP; PROTEIN AND SUBSTRATE D-TRP PREINCUBATED BEFORE PLATE SET-UP; DROP RATIO: 1:1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.3 | 62.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 138.91 | α = 90 |
b = 138.91 | β = 90 |
c = 142.59 | γ = 120 |
Symmetry | |
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Space Group | P 64 |
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 | 2017-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9164 | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 2.33 | 50 | 100 | 0.13 | 0.998 | 14.09 | 20.84 | 66588 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.33 | 2.39 | 100 | 1.71 | 0.746 | 1.96 | 21.05 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6H43 CHAINA | 2.33 | 49.8 | 66549 | 3342 | 100 | 0.192 | 0.237 | RANDOM | 70.03 |
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] | |
0.337 | 0.168 | 0.337 | -1.092 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.452 |
r_dihedral_angle_4_deg | 18.463 |
r_dihedral_angle_3_deg | 14.442 |
r_scangle_it | 8.624 |
r_scangle_other | 8.623 |
r_mcangle_it | 8.313 |
r_mcangle_other | 8.312 |
r_dihedral_angle_1_deg | 7.251 |
r_scbond_it | 6.163 |
r_scbond_other | 6.162 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8401 |
Nucleic Acid Atoms | |
Solvent Atoms | 224 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |