7MVS
DNA gyrase complexed with uncleaved DNA and Compound 7 to 2.6A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XCS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.2 | 298 | motherliquor: 80mM Bis-Tris, pH=6.2, 15.33% PEG 5000MME protein: 50mM HEPES, pH=7.5 1.2uL motherliquor : 0.8uL protein streaked with existing seed stock |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.01 | 59.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.017 | α = 90 |
b = 93.017 | β = 90 |
c = 406.663 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 77 | PIXEL | DECTRIS PILATUS3 6M | 2020-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.54 | APS | 19-ID |
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 | 2.601 | 23.7427486328 | 98.87 | 0.22 | 0.239 | 0.093 | 0.997 | 9.2 | 6.1 | 60022 | 61.3801855894 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.601 | 2.694 | 90.81 | 0.66 | 0.389 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | NONE | 2XCS | 2.60137142659 | 23.7427486328 | 1.33788961277 | 60022 | 3878 | 97.216123286 | 0.19732038353 | 0.195513593603 | 0.251722343658 | 77.4825563237 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.1374182196 |
f_angle_d | 0.507407405598 |
f_chiral_restr | 0.0401003713926 |
f_bond_d | 0.00329705531821 |
f_plane_restr | 0.00300558890709 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10627 |
Nucleic Acid Atoms | 800 |
Solvent Atoms | 145 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |