4HRQ
Identification of Function and Mechanistic Insights of Guanine Deaminase from Nitrosomonas europaea: Role of the C-terminal Loop in Catalysis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2G84 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 281 | 0.225M MgCl2, 25% PEG 3350, 0.1M Bis-tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 35.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.254 | α = 90 |
b = 74.123 | β = 90 |
c = 110.189 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RIGAKU RAXIS IV++ | 2012-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E DW | 0.97 |
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 | 1.82 | 50 | 99 | 0.057 | 17.7 | 5.3 | 28713 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.82 | 1.89 | 99 | 0.406 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2G84 | 1.9 | 50 | 24701 | 2445 | 97 | 0.2195 | 0.2463 | 20.0542 |
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] | |
-2.395 | 6.291 | -3.896 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
c_angle_d | 1.17 |
c_bond_d | 0.0046 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg | |
c_angle_deg_na | |
c_angle_deg_prot | |
c_dihedral_angle_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2743 |
Nucleic Acid Atoms | |
Solvent Atoms | 157 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
CNS | phasing |