6PTG
Structure of RNA polymerase binding protein and transcriptional regulator Dks from Chlamydia trachomatis L2 (LGV434)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4IJJ | MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s |
experimental model | PDB | 1TJL | MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s |
experimental model | PDB | 2KQ9 | MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s |
experimental model | PDB | 2KGO | MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s |
experimental model | PDB | 5W1S | MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Optimization screen HRCS_B5_PEG4000-3350, based on Hampton Research Crystal Screen B5, condition H3: 200mM Lithium sulfate, 25% (w/V) PEG 4000, 100mM Tris Base / HCl pH 8.5: ChtrB.19237.a.B1.PW38581 at 24mg/ml, grown at 14C: cryo: 15% EG: tray 310000 h3: puck lkp6-3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.32 | 63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.42 | α = 90 |
b = 83.42 | β = 90 |
c = 99.03 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | CCD | RAYONIX MX-300 | 2019-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.95 | 30.024 | 98.8 | 0.068 | 0.074 | 0.999 | 20.54 | 6.108 | 8668 | 63.378 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.95 | 3.03 | 98.9 | 0.625 | 0.682 | 0.89 | 3.12 | 6.225 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MR-Rosetta, using input from PDB codes 4ijj, 1tjl, 2kq9, 2kgo, and 5w1s | 2.95 | 30.024 | 1.36 | 8651 | 835 | 98.99 | 0.1866 | 0.1823 | 0.2264 | 0 | 73.7569 |
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 |
f_dihedral_angle_d | 13.278 |
f_angle_d | 0.542 |
f_chiral_restr | 0.039 |
f_bond_d | 0.004 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1270 |
Nucleic Acid Atoms | |
Solvent Atoms | 23 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MR-Rosetta | phasing |
Coot | model building |