4JZS
Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH (E68A mutant)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8.3 | 293 | 1.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, vapor diffusion, temperature 293K |
2 | VAPOR DIFFUSION | 8.3 | 293 | 1.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, soaking in 500 mM NaI during 30s, vapor diffusion, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.92 | α = 90 |
b = 116.92 | β = 90 |
c = 55.58 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2011-09-30 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2011-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.93340 | ESRF | ID14-1 |
2 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.93340 | ESRF | ID14-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 48.72 | 99.9 | 0.054 | 20.8 | 22194 | 22172 | -3 | -3 | 49.87 |
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) | |||||||||||
1,2 | 2.2 | 2.32 | 99.4 | 0.839 | 2 | 5.6 | 17999 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SIRAS | THROUGHOUT | 2.2 | 37.43 | 22157 | 1132 | 99.78 | 0.2142 | 0.2126 | 0.23 | 0.2446 | 0.26 | RANDOM | 59.5809 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
2.0839 | 2.0839 | -4.1678 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 19.17 |
t_omega_torsion | 2.33 |
t_angle_deg | 0.99 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2606 |
Nucleic Acid Atoms | |
Solvent Atoms | 58 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
SHARP | phasing |
BUSTER-TNT | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
XDS | data reduction |
XSCALE | data scaling |
BUSTER | refinement |