3O7H
Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Q37 | PDB ENTRY 2Q37 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | 22-26% PEG-8000, 0.25 M sodium acetate in pH 6.5 cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.799 | α = 113.18 |
b = 49.338 | β = 116.49 |
c = 51.687 | γ = 94.26 |
Symmetry | |
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Space Group | P 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 | 2010-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE A1 | 0.987 | CHESS | A1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.79 | 50 | 93.8 | 0.03 | 27.8 | 1.7 | 33900 | 31800 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.79 | 1.82 | 75 | 0.142 | 4.7 | 1.5 |
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 2Q37 | 1.79 | 23.13 | 30202 | 1603 | 93 | 0.22226 | 0.22104 | 0.24474 | RANDOM | 20.076 |
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] | |
0.06 | 0.05 | 0.04 | -0.01 | 0.05 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.943 |
r_dihedral_angle_4_deg | 16.681 |
r_dihedral_angle_3_deg | 13.25 |
r_dihedral_angle_1_deg | 3.804 |
r_scangle_it | 1.54 |
r_angle_refined_deg | 0.894 |
r_scbond_it | 0.866 |
r_mcangle_it | 0.582 |
r_mcbond_it | 0.295 |
r_chiral_restr | 0.055 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2527 |
Nucleic Acid Atoms | |
Solvent Atoms | 246 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |