6ZT3
N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZKB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | NULL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.985 | α = 90 |
b = 76.985 | β = 90 |
c = 261.476 | γ = 120 |
Symmetry | |
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Space Group | P 61 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 EIGER X 16M | 2019-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.56 | 65.37 | 100 | 0.141 | 0.143 | 0.023 | 1 | 16.7 | 38.8 | 66509 | 19.9 |
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 | 1.56 | 1.59 | 100 | 2.486 | 2.518 | 0.399 | 0.845 | 39.5 |
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 | 3ZKB | 1.56 | 64.69 | 63082 | 3287 | 99.99 | 0.1493 | 0.1469 | 0.1939 | RANDOM | 23.46 |
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] | |
-1.84 | -0.92 | -1.84 | 5.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.84 |
r_dihedral_angle_4_deg | 18.378 |
r_dihedral_angle_3_deg | 15.125 |
r_dihedral_angle_1_deg | 6.279 |
r_rigid_bond_restr | 3.043 |
r_angle_other_deg | 1.44 |
r_angle_refined_deg | 1.368 |
r_chiral_restr | 0.068 |
r_bond_refined_d | 0.007 |
r_bond_other_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3033 |
Nucleic Acid Atoms | |
Solvent Atoms | 302 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
PHASER | phasing |