6OW7
X-ray Structure of Polypeptide Deformylase with a Piperazic Acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 295 | 1 % - 4 % PEG400 45 % - 55% Ammonium Sulfate 0.1 M HEPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.229 | α = 90 |
b = 69.229 | β = 90 |
c = 91.879 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 173 | CCD | ADSC QUANTUM 210 | 2005-12-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.45 | 38.28 | 94 | 42.6 | 3.6 | 72134 | 20.58 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.45 | 1.5 | 66.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.45 | 38.28 | 1.35 | 72063 | 1992 | 94.27 | 0.2063 | 0.2059 | 0.2179 | 26.45 |
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 | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.5943 |
f_angle_d | 0.8085 |
f_chiral_restr | 0.0783 |
f_bond_d | 0.0058 |
f_plane_restr | 0.0047 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3031 |
Nucleic Acid Atoms | |
Solvent Atoms | 211 |
Heterogen Atoms | 70 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |