4OLP
Ligand-free structure of the GrpU microcompartment shell protein from Pectobacterium wasabiae
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 296 | 0.1M sodium/potassium phosphate, 30% 2-methyl-2,4-pentanediol, pH 6.0, vapor diffusion, hanging drop, temperature 296K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 41.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.845 | α = 90 |
b = 117.845 | β = 90 |
c = 76.023 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | PIXEL | DECTRIS PILATUS 6M-F | 2012-03-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97920 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.79 | 100 | 99.5 | 0.087 | 10.2 | 12.9 | 9715 |
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 | 2.79 | 2.9 | 97.5 | 0.602 | 6.1 | 937 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.79 | 60.97 | 9710 | 468 | 99.35 | 0.2178 | 0.2154 | 0.22 | 0.2671 | 0.27 | RANDOM | 99.336 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
-3.65 | -1.83 | -3.65 | 11.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.611 |
r_dihedral_angle_3_deg | 19.281 |
r_dihedral_angle_4_deg | 18.741 |
r_mcangle_it | 6.947 |
r_dihedral_angle_1_deg | 5.67 |
r_mcbond_it | 4.506 |
r_mcbond_other | 4.505 |
r_angle_refined_deg | 1.602 |
r_angle_other_deg | 1.446 |
r_chiral_restr | 0.091 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2637 |
Nucleic Acid Atoms | |
Solvent Atoms | 4 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |