1N9K
Crystal structure of the bromide adduct of AphA class B acid phosphatase/phosphotransferase from E. coli at 2.2 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 M solution of NaBr |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.36 | 63.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.499 | α = 90 |
b = 92.616 | β = 90 |
c = 138.247 | 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 | x-ray | 100 | IMAGE PLATE | MARRESEARCH | Torodial mirror | 2002-05-08 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X31 | 0.91957, 0.9204, 0.88561 | EMBL/DESY, HAMBURG | X31 |
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 | 2.2 | 20 | 98.2 | 0.092 | 0.092 | 8 | 4.17 | 32466 | 32466 | 24.13 |
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 | 2.23 | 96.6 | 0.33 | 3.9 | 3.3 | 1272 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.2 | 19.32 | 30818 | 30818 | 1648 | 98.3 | 0.19069 | 0.19069 | 0.18855 | 0.23111 | RANDOM | 26.068 |
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] | |
0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.186 |
r_scangle_it | 5.264 |
r_scbond_it | 3.392 |
r_mcangle_it | 2.031 |
r_angle_refined_deg | 1.901 |
r_mcbond_it | 1.186 |
r_symmetry_hbond_refined | 0.306 |
r_nbd_refined | 0.218 |
r_symmetry_vdw_refined | 0.203 |
r_xyhbond_nbd_refined | 0.168 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3286 |
Nucleic Acid Atoms | |
Solvent Atoms | 380 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | model building |
REFMAC | refinement |
RESOLVE | phasing |