7R1P
X-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au1 with RNase A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JVT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.1 | 293 | 22% PEG4K 10 mM sodium citrate pH 5.1 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.72 | α = 90 |
b = 32.72 | β = 90.261 |
c = 72.71 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2021-07-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 0.96 | ELETTRA | 11.2C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.42 | 50.36 | 96.1 | 0.073 | 0.08 | 0.031 | 0.998 | 12.9 | 6.4 | 43467 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.42 | 1.45 | 94.2 | 0.599 | 0.661 | 0.248 | 0.807 | 3.6 | 6.7 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1JVT | 1.42 | 50.36 | 43467 | 96.068 | 0.191 | 0.1893 | 0.219 | 23.39 |
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] | |
0.019 | 0.084 | -0.063 | 0.043 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.161 |
r_dihedral_angle_3_deg | 13.492 |
r_dihedral_angle_4_deg | 12.836 |
r_dihedral_angle_1_deg | 7.061 |
r_lrange_it | 6.924 |
r_lrange_other | 6.852 |
r_scangle_it | 4.526 |
r_scangle_other | 4.504 |
r_mcangle_it | 3.594 |
r_mcangle_other | 3.593 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1902 |
Nucleic Acid Atoms | |
Solvent Atoms | 257 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
autoPROC | data scaling |
PHASER | phasing |