1Q7Y
Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transferase center of the 50S ribosomal subunit
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JJ2 | PDB entry 1JJ2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.8 | PEG 6K, KCl, NaCl, MgCl2, NH4Cl, EG, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 100K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.17 | 61.14 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 212.902 | ¦Á = 90 |
b = 300.474 | ¦Â = 90 |
c = 575.176 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 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 | CUSTOM-MADE | 1999-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.0 | APS | 19-ID |
Data Collection
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 entry 1JJ2 | 3.2 | 19.99 | 299527 | 275912 | 2712 | 92.1 | 0.225 | 0.225 | 0.28 | RANDOM based on 1JJ2 | 56.8 |
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] | |
23.22 | -19.94 | -3.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 16.1 |
c_scangle_it | 2.02 |
c_mcangle_it | 1.89 |
c_improper_angle_d | 1.86 |
c_angle_deg | 1.7 |
c_scbond_it | 1.25 |
c_mcbond_it | 1.09 |
c_bond_d | 0.014 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 28801 |
Nucleic Acid Atoms | 61675 |
Solvent Atoms | 7871 |
Heterogen Atoms | 269 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNS | phasing |