8B6E
crystal structure of the DNA-binding short chromatophore-targeted protein sCTP-23166 from Paulinella chromatophora
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 285 | 0.1 M sodium HEPES pH 7.5, 15 % (w/v) PEG 20000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.56 | 21.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 28.887 | α = 83.99 |
b = 30.943 | β = 63.45 |
c = 31.188 | γ = 69.84 |
Symmetry | |
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Space Group | P 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 | PIXEL | DECTRIS EIGER X 16M | 2021-10-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.9200 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.2 | 29 | 93 | 0.06978 | 0.997 | 12.04 | 3.6 | 27013 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.2 | 1.243 | 0.945 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | alphafold | 1.2 | 29 | 25712 | 1310 | 95.39 | 0.1333 | 0.1312 | 0.1763 | RANDOM | 19.089 |
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] | |
1.39 | -0.81 | -2.21 | -3.17 | 1.51 | -0.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 24.377 |
r_dihedral_angle_4_deg | 14.958 |
r_dihedral_angle_3_deg | 11.252 |
r_rigid_bond_restr | 6.563 |
r_dihedral_angle_1_deg | 6.198 |
r_angle_refined_deg | 1.993 |
r_angle_other_deg | 1.543 |
r_chiral_restr | 0.103 |
r_bond_refined_d | 0.015 |
r_gen_planes_refined | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 802 |
Nucleic Acid Atoms | |
Solvent Atoms | 121 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
AutoProcess | data reduction |
AutoProcess | data scaling |
PHASER | phasing |