5E9R
X-ray structure of the complex between lysozyme and the compound fac, cis-[RuII(CO)3Cl2(N3-MBI), MBI=N-methyl-benzimidazole
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | Hen egg white lysozyme was incubated for 2 h in the presence of Ru-MBI in 1:10 protein to metal compound ratio. The adduct was then crystallized by using the hanging drop vapour diffusion method. Drops of 1 microliter were prepared at room temperature mixing 0.5 microliter of adduct at concentration 15 mg/mL with an equal amount of a reservoir constituted by 1.1 M NaCl, 0.1 M acetate buffer, pH 4.0. Crystals of the adduct grow within 24-48 hours. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 36.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.5 | α = 90 |
b = 78.5 | β = 90 |
c = 36.309 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | RIGAKU SATURN 944+ | 2014-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 2.25 | 55.5 | 99.4 | 0.085 | 12.9 | 6.2 | 5740 |
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 | 2.25 | 2.29 | 100 | 0.436 | 5 | 6.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | THROUGHOUT | 2.25 | 55.5 | 5452 | 261 | 99.41 | 0.15626 | 0.15228 | 0.23734 | RANDOM | 34.896 |
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] | |
-0.92 | -0.92 | 1.84 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.117 |
r_dihedral_angle_4_deg | 24.33 |
r_dihedral_angle_3_deg | 14.361 |
r_long_range_B_refined | 7.259 |
r_long_range_B_other | 7.131 |
r_dihedral_angle_1_deg | 6.725 |
r_scangle_other | 4.918 |
r_mcangle_other | 3.138 |
r_mcangle_it | 3.113 |
r_scbond_it | 3.047 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 159 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |