1PEW
High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 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 | 1CD0 | PDB ENTRY 1CD0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 298 | 0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.577 | α = 90 |
b = 73.577 | β = 90 |
c = 92.298 | γ = 90 |
Symmetry | |
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Space Group | P 41 2 2 |
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 | 113 | DIFFRACTOMETER | RIGAKU AFC-5R | 2001-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | 1.5418 | MPG/DESY, HAMBURG | BW6 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.6 | 15 | 97.3 | 0.066 | 20.2 | 13.3 | 32368 | 31495 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.6 | 1.66 | 93.8 | 0.515 | 5.4 | 11.3 | 3339 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1CD0 | 1.6 | 8 | 4 | 31495 | 1633 | 97.3 | 0.295 | 0.2533 | 0.2522 | 0.27291 | RANDOM | 12.751 |
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] | |
0.14 | 0.14 | -0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.962 |
r_scangle_it | 2.234 |
r_scbond_it | 1.565 |
r_angle_refined_deg | 1.29 |
r_mcangle_it | 0.904 |
r_mcbond_it | 0.53 |
r_symmetry_hbond_refined | 0.352 |
r_symmetry_vdw_refined | 0.334 |
r_xyhbond_nbd_other | 0.234 |
r_nbd_refined | 0.228 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1647 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |