3K1M
Crystal Structure of full-length BenM, R156H mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER OIL | 295 | 5mcL precipitant and 4 mcL protein solution. Precipitant: 80% Crystal Screen 2 (CS-2, Hampton Research) condition 31, 20% CS-2 condition 26 Protein: 30 mM Tris, 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM mercaptolethanol, pH 9.0, MICROBATCH UNDER OIL, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.24 | 62.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.997 | α = 90 |
b = 70.789 | β = 90 |
c = 186.275 | γ = 90 |
Symmetry | |
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Space Group | P 2 2 21 |
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 | CCD | MAR CCD 165 mm | 2009-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97934 | APS | 19-ID |
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 | 2.29 | 100 | 99.6 | 0.071 | 13.7 | 5.6 | 41907 | 25.981 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.29 | 2.34 | 100 | 0.507 | 0.507 | 3.81 | 5.7 | 2078 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2F97 | 2.29 | 49.77 | 41729 | 41729 | 2116 | 97.84 | 0.148 | 0.148 | 0.147 | 0.179 | RANDOM | 25.981 |
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] | |
9.18 | 15.41 | -24.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.775 |
r_dihedral_angle_4_deg | 14.267 |
r_dihedral_angle_3_deg | 13.942 |
r_dihedral_angle_1_deg | 4.949 |
r_mcangle_it | 2.746 |
r_mcbond_it | 1.987 |
r_scangle_it | 1.369 |
r_angle_refined_deg | 1.037 |
r_scbond_it | 0.956 |
r_chiral_restr | 0.068 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4836 |
Nucleic Acid Atoms | |
Solvent Atoms | 508 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data collection |