6YRD
SFX structure of dye-type peroxidase DtpB in the ferryl state
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7.5 | 293 | 6-10 mg/mL of protein in 50mM Sodium acetate, 150mM NaCl pH 5 was mixed with 150 mM MgCl2, 150 mM HEPES, 20% PEG 4000 pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 50.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 86.3 | α = 90 |
b = 120 | β = 90 |
c = 198.45 | γ = 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 | 301 | CCD | MPCCD | 2019-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SACLA BEAMLINE BL2 | 1.13 | SACLA | BL2 |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | silicon chip | fixed target |
Fixed Target | ||||||
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Sample Solvent | |
1 | silicon chip | 25600 apertures per chip |
Measurement | |||||
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 10 | 11 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (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 | 1.75 | 102 | 100 | 0.984 | 0.109 | 6.1 | 1943 | 207440 | 28.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.75 | 1.8 | 0.423 | 0.887 |
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 | unpublished structure | 1.75 | 13 | 196370 | 10353 | 99.67 | 0.1682 | 0.1666 | 0.1988 | RANDOM | 33.628 |
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] | |
0.23 | -0.36 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.319 |
r_dihedral_angle_4_deg | 17.361 |
r_dihedral_angle_3_deg | 13.019 |
r_dihedral_angle_1_deg | 6.771 |
r_angle_refined_deg | 1.626 |
r_angle_other_deg | 1.445 |
r_chiral_restr | 0.073 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.009 |
r_gen_planes_other | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13904 |
Nucleic Acid Atoms | |
Solvent Atoms | 880 |
Heterogen Atoms | 279 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
CrystFEL | data scaling |
REFMAC | phasing |