6VR8
Structure of a pseudomurein peptide ligase type E from Methanothermus fervidus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.4 | 293 | 0.2 M ammonium sulfate, 30% w/v PEG4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.369 | α = 90 |
b = 119.369 | β = 90 |
c = 71.088 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 210r | 2016-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX1 | 0.9537 | Australian Synchrotron | MX1 |
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 | 1.9 | 41.8 | 100 | 0.102 | 0.997 | 14.6 | 22 | 45561 | 21.36 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.94 | 1.94 | 0.884 | 4.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.9 | 39.07 | 1.33 | 45498 | 2381 | 99.94 | 0.1874 | 0.1848 | 0.18 | 0.2328 | 0.23 | 26.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.5751 |
f_angle_d | 0.7583 |
f_chiral_restr | 0.0524 |
f_bond_d | 0.005 |
f_plane_restr | 0.0048 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3789 |
Nucleic Acid Atoms | |
Solvent Atoms | 402 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |