7N6S
Crystal Structure of deoxyuridine 5'-triphosphate nucleotidohydrolase from Rickettsia prowazekii str. Madrid E in complex with 2'-deoxyuridine 5'-monophoephate (dUMP)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7N56 | pdb entry 7n56, apo structure |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 287 | Anatrace / Calibre MCSG1 screen, condition H9: 100mM BisTris /HCl pH 5.5, 25% (w/V) PEG 3350: RiprA.10050.a.A1.PS00480 at 24mg/ml + 5mM dUMP / MgCl2: tray 320891 h9: cryo: 20% glycerol + compounds: puck bqq7-7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.72 | α = 90 |
b = 87 | β = 90 |
c = 183.34 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 6M | 2021-05-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
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 | 1.75 | 50 | 99.8 | 0.036 | 0.039 | 1 | 30.17 | 7.073 | 82624 | 32.944 |
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 | 1.75 | 1.8 | 99.9 | 0.485 | 0.533 | 0.881 | 3.23 | 5.944 |
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 | FREE R-VALUE | pdb entry 7n56, apo structure | 1.75 | 45.83 | 1.34 | 82611 | 2043 | 99.81 | 0.1725 | 0.1717 | 0.2053 | 0 | 32.66 |
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 | 11.7667 |
f_angle_d | 0.9051 |
f_chiral_restr | 0.0642 |
f_plane_restr | 0.0087 |
f_bond_d | 0.0077 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6384 |
Nucleic Acid Atoms | |
Solvent Atoms | 664 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Coot | model building |
PHENIX | model building |