H/D exchanged Hen egg-white lysozyme denatured in acidic conditions and refolded in solution
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | | 293 | NACL, SODIUM ACETATE-D3, ACETIC ACID-D4 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.07 | 40.66 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 79.182 | α = 90 |
b = 79.182 | β = 90 |
c = 37.906 | γ = 90 |
Symmetry |
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Space Group | P 43 21 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU RAXIS VII | | 2018-02-13 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | | 2018-03-19 | L | LAUE |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | ROTATING ANODE | RIGAKU | 1.54 | | |
2 | NUCLEAR REACTOR | ORNL High Flux Isotope Reactor BEAMLINE CG4D | 2.8-4.5 | ORNL High Flux Isotope Reactor | CG4D |
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) | CC (Half) | R Split (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 |
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1 | 2 | 100 | 99.6 | 0.027 | | | | | | 67.6 | 14.5 | | 8580 | | | 23.63 |
2 | 2 | 100 | 91 | 0.166 | | | | | | 6.5 | 8.5 | | 7546 | | | 23.63 |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2 | 2.07 | | 0.08 | | | | | | | | |
2 | 2 | 2.11 | | 0.268 | | | | | | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | 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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 39.59 | | 1.37 | | 8542 | 418 | 99.62 | | 0.1425 | 0.1403 | 0.1829 | | 22.41 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 55.99 | | | | 7546 | | 91 | | | 0.2328 | 0.2656 | | |
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] |
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| | | | | |
| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 18.2902 |
f_angle_d | 0.8166 |
f_chiral_restr | 0.0542 |
f_bond_d | 0.0058 |
f_plane_restr | 0.0043 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 997 |
Nucleic Acid Atoms | |
Solvent Atoms | 86 |
Heterogen Atoms | 2 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |