H/D exchanged Hen egg-white lysozyme
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 193L | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | NaCl, sodium acetate-d3, acetic acid-d4, 100% D2O |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.06 | 40.41 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 79.094 | α = 90 |
| b = 79.094 | β = 90 |
| c = 37.828 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 43 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | IMAGE PLATE | RIGAKU | | 2018-02-13 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | MAATEL IMAGINE | | 2018-09-20 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 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 |
|---|
| 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 |
|---|
| 1 | 2 | 100 | 93.3 | 0.058 | | 0.059 | 0.011 | | | 63.5 | 25.2 | | 8051 | | | 23.64 |
| 2 | 2 | 34.12 | 87.8 | 0.163 | | 0.174 | 0.059 | | | 5.5 | 6.4 | | 7338 | | | |
| Highest Resolution Shell |
|---|
| 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) |
|---|
| 1 | 2 | 2.07 | | 0.115 | | 0.118 | 0.024 | | | 26.2 | 22 | |
| 2 | 2 | 2.11 | | 0.29 | | 0.315 | 0.119 | | | 3.1 | 5.1 | |
Refinement
| Statistics |
|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 34.13 | | 1.44 | | 8026 | 397 | 93.46 | | 0.1342 | 0.1319 | 0.13 | 0.1798 | 0.18 | 1 | 23.26 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 34.12 | | | | 7338 | 647 | 87.7 | | | 0.2251 | | 0.2554 | | 1 | |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 17.6318 |
| f_dihedral_angle_d | 17.6318 |
| f_angle_d | 1.3201 |
| f_angle_d | 1.3201 |
| f_chiral_restr | 0.1031 |
| f_chiral_restr | 0.1031 |
| f_plane_restr | 0.0152 |
| f_plane_restr | 0.0152 |
| f_bond_d | 0.0132 |
| f_bond_d | 0.0132 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 997 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 87 |
| Heterogen Atoms | 2 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
