3M05
The crystal structure of a functionally unknown protein PEPE_1480 from Pediococcus pentosaceus ATCC 25745
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 277 | 0.2M Li2SO4, 0.1M MES, 20% (v/v)1,4-butanodiol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.55 | 77.86 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 119.774 | ¦Á = 90 |
b = 119.774 | ¦Â = 90 |
c = 119.349 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 43 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 | ADSC QUANTUM 315r | Mirror | 2010-02-04 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97937, 0.97951 | APS | 19-ID |
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 | 3.145 | 37.862 | 99.7 | 0.109 | 27.2 | 7 | 15624 | 15624 |
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 | 3.15 | 3.2 | 100 | 0.804 | 2.4 | 7.2 | 749 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 3.145 | 37.862 | 0.05 | 14772 | 14772 | 739 | 94.57 | 0.1985 | 0.1985 | 0.196 | 0.2468 | 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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.087 |
f_angle_d | 1.295 |
f_chiral_restr | 0.076 |
f_bond_d | 0.01 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2317 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms | 30 |
Software
Software | |
---|---|
Software Name | Purpose |
SBC-Collect | data collection |
SHELXD | phasing |
MLPHARE | phasing |
DM | model building |
RESOLVE | model building |
HKL-3000 | phasing |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |
RESOLVE | phasing |