3CZ4
Native AphA class B acid phosphatase/phosphotransferase from E. coli
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2B82 | PDB entry 2B82 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 279 | drop: 4.2-3.5 mg/mL in 50 mM CH3COONa buffer at pH 7.2, 10 mM MgCl2 reservoir: 18% (w/v) polyethylene glycol (PEG) 6000, 0.6% (w/v) Spermine, VAPOR DIFFUSION, SITTING DROP, temperature 279K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.34 | 63.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.294 | α = 90 |
b = 92.775 | β = 90 |
c = 137.6 | 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 | Monochromator double crystal, Si(111); toroidal mirror | 2002-07-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.934 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.7 | 8 | 96.8 | 0.092 | 4.4 | 4.3 | 31967 | 2 | 17.14 |
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) | ||||||||||
1.7 | 1.742 | 99.51 | 0.165 | 0.165 | 2.3 | 4.14 | 2311 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | PDB entry 2B82 | 1.7 | 7.99 | 2 | 31967 | 31967 | 1717 | 96.84 | 0.181 | 0.181 | 0.181 | 0.21167 | RANDOM | 23.54 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.098 |
r_dihedral_angle_4_deg | 18.695 |
r_dihedral_angle_3_deg | 12.224 |
r_dihedral_angle_1_deg | 4.99 |
r_scangle_it | 2.86 |
r_scbond_it | 1.79 |
r_mcangle_it | 1.176 |
r_angle_refined_deg | 1.082 |
r_mcbond_it | 0.692 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1680 |
Nucleic Acid Atoms | |
Solvent Atoms | 324 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
MOLREP | phasing |