2V06
Crystal structure of the PPM Ser-Thr phosphatase MsPP from Mycobacterium smegmatis at pH 5.5
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 5.5 | pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 40.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.718 | α = 90 |
b = 83.596 | β = 90 |
c = 33.638 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | MARRESEARCH | MIRRORS | 2006-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7A | EMBL/DESY, HAMBURG | BW7A |
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 | 1.05 | 15 | 98.8 | 0.03 | 11.3 | 2.7 | 97914 |
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 | 1.05 | 1.1 | 99.2 | 0.41 | 2.7 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | OTHER | FREE R-VALUE | 1.05 | 6 | 97463 | 4873 | 98.8 | 0.1328 | 0.1314 | 0.1875 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
81 | 1634 | 2062.17 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.1 |
s_zero_chiral_vol | 0.088 |
s_non_zero_chiral_vol | 0.08 |
s_similar_adp_cmpnt | 0.06 |
s_anti_bump_dis_restr | 0.046 |
s_angle_d | 0.035 |
s_from_restr_planes | 0.0286 |
s_bond_d | 0.014 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1706 |
Nucleic Acid Atoms | |
Solvent Atoms | 387 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
SHELXL-97 | refinement |
XDS | data reduction |
XSCALE | data scaling |