2EK8
Aminopeptidase from Aneurinibacillus sp. strain AM-1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 5.8 | 299 | 13% PEG 8000, 0.1M MES-NaOH, 0.2M Zinc acetate, pH 5.8, VAPOR DIFFUSION, temperature 299K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.85 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 93.624 | α = 90 |
b = 68.618 | β = 90 |
c = 76.841 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 93 | IMAGE PLATE | RIGAKU RAXIS VII | 2006-07-06 | |||||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL44B2 | 0.9792, 0.9788, 0.9639 | SPring-8 | BL44B2 |
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 | ||||||||
2 | 1.8 | 19.9 | 98.7 | 0.058 | 31.2 | 10.6 | 45919 | 18.5 |
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) | |||||||||||
2 | 1.8 | 1.9 | 97.1 | 0.336 | 6.1 | 10.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.8 | 19.85 | 45812 | 2292 | 98.2 | 0.213 | 0.213 | 0.238 | RANDOM | 28.1 |
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] | |
-0.06 | -0.19 | 0.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.6 |
c_scangle_it | 2.68 |
c_scbond_it | 2.01 |
c_mcangle_it | 1.54 |
c_angle_deg | 1.1 |
c_mcbond_it | 0.96 |
c_improper_angle_d | 0.77 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3119 |
Nucleic Acid Atoms | |
Solvent Atoms | 517 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CrystalClear | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
SOLVE | phasing |