6LON
Crystal structure of HPSG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5YMR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291.15 | 0.2M sodium acetate, 0.1M Bis-Tris propane, pH 6.5, 16% (w/v) PEG 3350, 500mM DHPS |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.917 | α = 90 |
b = 219.401 | β = 98.04 |
c = 213.141 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 193.15 | PIXEL | DECTRIS PILATUS3 R CdTe 300K | 2019-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.9792 | SSRF | BL18U1 |
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) | 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 | 2.198 | 50 | 99.9 | 0.086 | 0.102 | 0.055 | 3.7 | 3.4 | 213322 | 25.21 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.2 | 2.24 | 99.9 | 0.442 | 0.525 | 0.281 | 0.794 | 3.4 |
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 | THROUGHOUT | 5YMR | 2.2 | 36.248 | 1.37 | 213128 | 1999 | 99.73 | 0.143 | 0.1426 | 0.179 | 33.4472 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.558 |
f_angle_d | 1.087 |
f_chiral_restr | 0.055 |
f_bond_d | 0.011 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 25365 |
Nucleic Acid Atoms | |
Solvent Atoms | 2057 |
Heterogen Atoms | 780 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
PHENIX | phasing |