3NIO
Crystal structure of Pseudomonas aeruginosa guanidinobutyrase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GQ7 | PDB ENTRY 1GQ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 297 | 10mM cobalt(II) chloride, 0.1M MES at pH 6.5, 1.8M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.44 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.047 | α = 90 |
b = 158.954 | β = 114.84 |
c = 84.547 | 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 | ADSC QUANTUM 210 | 2006-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 6B | 1.0626 | PAL/PLS | 6B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2 | 20 | 99.9 | 0.097 | 24.4 | 133054 |
Refinement
Statistics | |||||||||||||||||||
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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 1GQ7 | 2 | 20 | 125264 | 6635 | 99.88 | 0.23409 | 0.23321 | 0.25105 | RANDOM | 22.647 |
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] | |
-0.33 | 0.97 | -1.46 | 2.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.594 |
r_dihedral_angle_4_deg | 13.634 |
r_dihedral_angle_3_deg | 13.482 |
r_dihedral_angle_1_deg | 4.994 |
r_angle_refined_deg | 1.216 |
r_scangle_it | 0.803 |
r_scbond_it | 0.464 |
r_mcangle_it | 0.35 |
r_mcbond_it | 0.186 |
r_chiral_restr | 0.079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14514 |
Nucleic Acid Atoms | |
Solvent Atoms | 1004 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
CNS | refinement |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |