4DXB
2.29A structure of the engineered MBP TEM-1 fusion protein RG13 in complex with zinc, P1 space group
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | A 1.0 uL drop was prepared using 0.5 uL protein mixture (13.8 mg/mL RG13, 2.5 mM zinc chloride) and 0.5 uL reservoir solution (0.2 M ammonium acetate, 0.1 M Tris, pH 8.5-9.5, 15-30% PEG3350) and equilibrated over a 1 ml reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 52.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.316 | α = 83.54 |
b = 74.177 | β = 77.64 |
c = 103.13 | γ = 89.98 |
Symmetry | |
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Space Group | P 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 | CCD | ADSC QUANTUM 315 | mirrors | 2007-01-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.0810 | NSLS | X29A |
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 | 31.45 | 56.8 | 0.054 | 1.9 | 62117 | 59138 | 1 | 38.4 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.29 | 2.38 | 95.5 | 0.223 | 3.8 | 1.9 | 5876 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRIES 1ZG4 AND 1OMP | 2.29 | 31.45 | 59138 | 56130 | 3008 | 95.2 | 0.23492 | 0.23183 | 0.29166 | RANDOM | 34.401 |
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] | |
-0.04 | -0.01 | -0.01 | 0.01 | 0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.971 |
r_dihedral_angle_3_deg | 15.174 |
r_dihedral_angle_4_deg | 12.709 |
r_dihedral_angle_1_deg | 4.515 |
r_mcangle_it | 2.551 |
r_scangle_it | 2.253 |
r_mcbond_it | 1.605 |
r_scbond_it | 1.505 |
r_angle_refined_deg | 0.96 |
r_nbtor_refined | 0.293 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9834 |
Nucleic Acid Atoms | |
Solvent Atoms | 490 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |