4LY3
Crystal structure of WlaRD, a sugar 3N-formyl transferase in the presence of dTPD-Qui3N, dTDP-Qui3NFo, and THF
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4LXQ | pdb entry 4LXQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | 11-15% PEG 8000, 200 mM NaCl, 5 mM TDP, 5 mM N-5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.12 | 60.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96.003 | α = 90 |
b = 65.552 | β = 109.83 |
c = 134.501 | 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 | CCD | Bruker Platinum 135 | mirrors | 2013-05-20 | 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 | 1.9 | 50 | 92.8 | 0.05 | 0.05 | 15.9 | 3.6 | 58443 | 58443 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 4LXQ | 1.9 | 50 | 58443 | 55503 | 2940 | 91.9 | 0.17999 | 0.17758 | 0.22617 | RANDOM | 18.94 |
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] | |
0.32 | -0.06 | 0.82 | -0.88 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.692 |
r_dihedral_angle_3_deg | 13.626 |
r_dihedral_angle_4_deg | 13.25 |
r_dihedral_angle_1_deg | 7.464 |
r_angle_refined_deg | 1.99 |
r_angle_other_deg | 0.881 |
r_chiral_restr | 0.116 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.01 |
r_gen_planes_other | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4472 |
Nucleic Acid Atoms | |
Solvent Atoms | 609 |
Heterogen Atoms | 162 |
Software
Software | |
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Software Name | Purpose |
APEX | data collection |
PHASER | phasing |
REFMAC | refinement |
APEX | data reduction |