7CY7
Crystal Structure of CMD1 in complex with DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7CY4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 290 | 15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 153.613 | α = 90 |
b = 125.764 | β = 102.82 |
c = 64.034 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | PIXEL | DECTRIS PILATUS3 S 6M | 2020-05-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NFPSS BEAMLINE BL19U1 | 0.9785 | NFPSS | BL19U1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.15 | 50.01 | 96.7 | 0.067 | 1 | 15.8 | 6.6 | 60566 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.15 | 2.21 | 0.52 | 0.82 | 2 |
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 | 7CY4 | 2.15 | 50.01 | 57529 | 3035 | 94.05 | 0.1896 | 0.1879 | 0.2206 | RANDOM | 40.4 |
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] | |
2.87 | -0.62 | -3.82 | 1.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.815 |
r_sphericity_free | 26.609 |
r_sphericity_bonded | 20.093 |
r_dihedral_angle_4_deg | 19.479 |
r_dihedral_angle_3_deg | 14.943 |
r_dihedral_angle_1_deg | 5.596 |
r_rigid_bond_restr | 3.986 |
r_angle_refined_deg | 1.118 |
r_angle_other_deg | 0.993 |
r_chiral_restr | 0.055 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6624 |
Nucleic Acid Atoms | 327 |
Solvent Atoms | 402 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
PHENIX | phasing |