4XD1
X-ray structure of the N-formyltransferase QdtF from Providencia alcalifaciens, W305A mutant, in the presence of TDP-Qui3N and N5-THF
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4XCZ | PDB entry 4XCZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 293 | 5-7% PEG 8000, 100 mM HEPPS, 200 mM NaCl, 200 mM KCl, 5 mM TDP, 5 mM N5-THF |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.279 | α = 90 |
b = 78.279 | β = 90 |
c = 151.105 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | CCD | Bruker Platinum 135 | 2014-08-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 1.5 | 50 | 97 | 0.069 | 0.069 | 11.2 | 4.6 | 73582 | 73582 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.5 | 1.54 | 90.5 | 0.364 | 2.3 | 2.5 |
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 | PDB entry 4XCZ | 1.5 | 35.03 | 69887 | 3695 | 97.01 | 0.18124 | 0.17981 | 0.20828 | RANDOM | 18.299 |
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] | |
0.55 | 0.55 | -1.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.08 |
r_dihedral_angle_4_deg | 14.143 |
r_dihedral_angle_3_deg | 12.942 |
r_dihedral_angle_1_deg | 6.479 |
r_angle_refined_deg | 2.084 |
r_angle_other_deg | 0.932 |
r_chiral_restr | 0.126 |
r_bond_refined_d | 0.011 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3227 |
Nucleic Acid Atoms | |
Solvent Atoms | 605 |
Heterogen Atoms | 97 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |
PHASER | phasing |