6MG4
Structure of full-length human lambda-6A light chain JTO
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LIL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 296 | Crystals of JTO-FL were grown via sitting-drop vapor diffusion using a crystallization buffer consisting of 20% PEG 3350 and 0.2 M NH4H2PO4 at 23 degrees C. Both diamond-shaped and plate-shaped crystals were generated in the same drop using these conditions, but only the plate-shaped crystals produced usable diffraction data. Crystals were harvested and immediately flash cooled in liquid nitrogen. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.385 | α = 90 |
b = 82.464 | β = 90 |
c = 97.017 | 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 | 80 | PIXEL | DECTRIS PILATUS3 6M | 2018-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 1.0332 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rpim I (All) | 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 | 1.75 | 44.66 | 97.5 | 0.055 | 0.034 | 0.96 | 18.2 | 3.5 | 50814 | 28 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.75 | 1.78 | 86.2 | 0.49 | 0.29 | 0.84 | 2.1 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1LIL | 1.75 | 44.66 | 48204 | 2560 | 97.29 | 0.173 | 0.171 | 0.221 | RANDOM | 37 |
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] | |
-1.82 | 4.41 | -2.59 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.151 |
r_dihedral_angle_4_deg | 15.595 |
r_dihedral_angle_3_deg | 12.31 |
r_long_range_B_refined | 9.424 |
r_long_range_B_other | 9.203 |
r_dihedral_angle_1_deg | 7.173 |
r_scangle_other | 6.443 |
r_mcangle_it | 4.248 |
r_mcangle_other | 4.247 |
r_scbond_it | 4.182 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3257 |
Nucleic Acid Atoms | |
Solvent Atoms | 664 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |