7P6F
1.93 A resolution X-ray crystal structure of the transcriptional regulator SrnR from Streptomyces griseus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 8.5 | 293 | 1 uL of SrnR 12.5 mg mL-1 (in 20 mM TrisHCl PH 7.5, 150 mM NaCl, 1 mM TCEP) were added to 20 uL of volatile oil, immediately followed by 1 uL of precipitant containing 0.2 M calcium acetate hydrate, 0.1 M TrisHCl 8.5, 15 % w/v PEG 4000 (G6 condition of CSSII screening by Molecular Dimensions). |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.358 | α = 90 |
b = 113.358 | β = 90 |
c = 124.943 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 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 | 2019-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.97622 | PETRA III, EMBL c/o DESY | P13 (MX1) |
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 | 1.93 | 124.94 | 100 | 0.126 | 0.138 | 0.041 | 0.999 | 11.6 | 11.4 | 36223 | 26.8 |
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 | 1.93 | 1.98 | 100 | 1.67 | 1.827 | 0.541 | 0.633 | 1.5 | 11.7 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3F6V | 1.93 | 51.67 | 36181 | 1789 | 99.975 | 0.18 | 0.178 | 0.2167 | 38.772 |
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] | |
0.454 | 0.227 | 0.454 | -1.471 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.194 |
r_dihedral_angle_4_deg | 20.272 |
r_dihedral_angle_3_deg | 15.555 |
r_lrange_it | 7.495 |
r_lrange_other | 7.461 |
r_dihedral_angle_1_deg | 6.172 |
r_scangle_it | 4.527 |
r_scangle_other | 4.526 |
r_mcangle_it | 3.937 |
r_mcangle_other | 3.936 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3075 |
Nucleic Acid Atoms | |
Solvent Atoms | 347 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |