1VC8
Crystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 0.1M HEPES, 1.0M succinic acid, 1%(w/v) PEG 2000 MME, 4mM Ap6A, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.82 | 56.46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.413 | α = 90 |
b = 54.775 | β = 90 |
c = 111.673 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS VII | 2003-11-17 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E | 1.5418, 0.9744, 0.9792, 0.9798, 0.9819 |
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 | 50 | 99.9 | 0.032 | 42.3 | 22476 | 3 | 9.9 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2 | 2.07 | 100 | 0.078 | 23.5 |
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 | 2 | 19.96 | 22254 | 2212 | 99.3 | 0.195 | 0.195 | 0.225 | RANDOM | 18.2 |
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] | |
6.93 | -2.46 | -4.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23 |
c_scangle_it | 3.02 |
c_scbond_it | 2.03 |
c_angle_deg | 1.9 |
c_mcangle_it | 1.82 |
c_mcbond_it | 1.23 |
c_improper_angle_d | 0.96 |
c_bond_d | 0.009 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2002 |
Nucleic Acid Atoms | |
Solvent Atoms | 237 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MLPHARE | phasing |