H/D exchanged Hen egg-white lysozyme denatured in heat condition 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, 100% D2O, PH 4.6, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.07 | 40.61 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 79.15 | α = 90 |
b = 79.15 | β = 90 |
c = 37.902 | 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 | | 2018-02-16 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | | 2018-05-25 | 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 | 98.7 | 0.055 | | | | | | 42.1 | 13.6 | | 8521 | | | 24 |
2 | 2 | 100 | 86.4 | 0.169 | | | | | | 5 | 5.4 | | 7100 | | | 24 |
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 | | 0.139 | | | | | | | | |
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 | 39.58 | | 1.4 | | 8490 | 420 | 98.72 | | 0.1428 | 0.1408 | 0.1817 | 1 | 22.1 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 34.18 | | | | 7100 | | 86.4 | | | 0.224 | 0.2496 | | |
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 | 17.9836 |
f_angle_d | 0.8353 |
f_chiral_restr | 0.0574 |
f_plane_restr | 0.0128 |
f_bond_d | 0.0058 |
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 |