1N8N
Crystal structure of the Au3+ complex of AphA class B acid phosphatase/phosphotransferase from E. coli at 1.69 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 293 | AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K. The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 mM solution of AuCl3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.34 | 63.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.279 | α = 90 |
b = 92.457 | β = 90 |
c = 138.182 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | x-ray | 100 | CCD | ADSC QUANTUM 4 | Toroidal mirror | 2002-07-13 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 1.0377, 1.0404, 0.9392 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.69 | 46.13 | 88.8 | 0.061 | 0.061 | 7 | 3.7 | 31884 | 31884 | 19.709 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.69 | 1.79 | 53 | 0.093 | 0.093 | 7 | 1.6 | 2976 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | MAD-phased Bromine derivative at 2.2 A resolution | 1.69 | 46.13 | 31884 | 31884 | 1673 | 88.8 | 0.17906 | 0.17906 | 0.17759 | 0.20698 | RANDOM | 20.602 |
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] | |
1.63 | -0.72 | -0.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.605 |
r_scangle_it | 4.623 |
r_scbond_it | 2.695 |
r_mcangle_it | 1.634 |
r_angle_refined_deg | 1.412 |
r_mcbond_it | 0.898 |
r_symmetry_vdw_refined | 0.234 |
r_symmetry_hbond_refined | 0.223 |
r_nbd_refined | 0.197 |
r_xyhbond_nbd_refined | 0.148 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1643 |
Nucleic Acid Atoms | |
Solvent Atoms | 284 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |
REFMAC | refinement |
CCP4 | data scaling |