5TWK
Crystal Structure of RlmH in Complex with Sinefungin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NS5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289.15 | 0.1 M Tris-bicine buffer (pH 8.5), 0.09 M NaF, 0.09 M NaBr, 0.09 M NaI, 20% v/v PEG 550 MME, 10% w/v PEG 20,000 in the presence of 2 mM Sinefungin |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.37 | α = 90 |
b = 37.95 | β = 105.74 |
c = 121.82 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS PILATUS 6M-F | 2013-11-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.9792 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.1 | 39.1 | 99.24 | 0.06791 | 0.999 | 17.66 | 5.6 | 34496 |
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 | 2.1 | 2.18 | 93.52 | 0.886 | 1.95 | 5.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | NONE | 1NS5 | 2.1 | 39.084 | 1.37 | 34486 | 1725 | 99.21 | 0.1861 | 0.1833 | 0.238 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.973 |
f_angle_d | 1.274 |
f_chiral_restr | 0.085 |
f_bond_d | 0.013 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4960 |
Nucleic Acid Atoms | |
Solvent Atoms | 210 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |