6S1W
Crystal structure of dimeric M-PMV protease D26N mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 292 | Protein solution: 4.1 mg/mL protein, 5 mM TCEP, 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M sodium citrate buffer, 15% propan-2-ol, 5 mM TCEP; |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.987 | α = 90 |
b = 29.571 | β = 102.52 |
c = 85.2 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 2013-03-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.98 | 48.91 | 98.9 | 0.119 | 0.139 | 0.997 | 8.24 | 3.62 | 17123 | 25 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.98 | 2.1 | 94.3 | 0.627 | 0.737 | 0.521 | 2.03 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6S1U, chain A | 1.98 | 48.8 | 16122 | 1000 | 98.9 | 0.20313 | 0.19956 | 0.26063 | RANDOM | 34.024 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.18 | 0.22 | -2.45 | -0.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.09 |
r_dihedral_angle_3_deg | 16.612 |
r_dihedral_angle_4_deg | 14.287 |
r_dihedral_angle_1_deg | 8.13 |
r_long_range_B_refined | 6.31 |
r_long_range_B_other | 6.257 |
r_scangle_other | 3.085 |
r_mcangle_other | 2.991 |
r_mcangle_it | 2.988 |
r_scbond_it | 1.977 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1648 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |