6VJ2
3.10 Angstrom Resolution Crystal Structure of Foldase Protein (PrsA) from Lactococcus lactis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 292 | Protein: 6.4 mg/ml, 0.01M Tris HCl (pH 8.3); Reservoir (PEGs II screen, B6): 0.1M HEPES (pH 7.5), 20% (w/v) PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 56.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.513 | α = 90 |
b = 117.609 | β = 90 |
c = 149.31 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | MARMOSAIC 300 mm CCD | C(111) | 2018-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 3.1 | 30 | 99.9 | 0.122 | 0.122 | 0.137 | 0.061 | 13.7 | 4.9 | 26817 | -3 | 66.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 3.1 | 3.15 | 100 | 0.776 | 0.776 | 0.867 | 0.381 | 0.787 | 2.1 | 5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 3.1 | 29.4 | 25380 | 1307 | 99.77 | 0.2364 | 0.2337 | 0.2897 | RANDOM | 72.399 |
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] | |
2.58 | -2.27 | -0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 21.586 |
r_dihedral_angle_4_deg | 13.201 |
r_dihedral_angle_3_deg | 7.371 |
r_dihedral_angle_1_deg | 1.425 |
r_angle_refined_deg | 1.241 |
r_angle_other_deg | 0.327 |
r_gen_planes_refined | 0.054 |
r_chiral_restr | 0.053 |
r_gen_planes_other | 0.052 |
r_bond_refined_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8456 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |