4ZR8
Structure of uroporphyrinogen decarboxylase from Acinetobacter baumannii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.65 | 290 | native: Microlytics MGSC1 screen, B11: 18% PEG8000, 200 mM magnesium chloride, 100 mM Tris-HCl, pH 7.65, 11 mg/mL AcbaC.001152.a.B1.PW3767 + 2 mM NAD, cryoprotectant: 20% ethylene glycol, tray 262775, puck kzo2-10 |
2 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | iodide: Microlytics MGSC1 screen, A12: 20% PEG4000, 200 mM calcium chloride, 100 mM Tris-HCl, pH 8.5, 11 mg/mL AcbaC.001152.a.B1.PW3767 + 2 mM NAD, cryoprotectant: 10% ethylene glycol + 250 mM sodium iodide, then 20% ethylene glycol + 500 mM sodium iodide, tray 262775, puck hml1-17 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44 |
2.21 | 44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.54 | α = 90 |
b = 83.38 | β = 106.97 |
c = 68.46 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RAYONIX MX-300 | 2015-04-16 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | 100 | CCD | RIGAKU SATURN 944+ | 2015-04-17 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 99.8 | 0.038 | 0.044 | 20.9 | 3.8 | 112341 | -3 | 15.13 |
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) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.5 | 1.54 | 99.8 | 0.448 | 0.524 | 2.89 | 3.73 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R-VALUE | 1.5 | 28.805 | 1.36 | 112318 | 5705 | 99.85 | 0.1306 | 0.129 | 0.1609 | Random selection | 22.1475 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
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 | 12.768 |
f_angle_d | 1.037 |
f_chiral_restr | 0.046 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5422 |
Nucleic Acid Atoms | |
Solvent Atoms | 805 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
ARP | model building |
Coot | model building |
PHENIX | refinement |