Joint Xray/Neutron structure of human DJ-1 at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1P5F | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289 | 20% PEG3350, 100 mM HEPES pH=7.5 and 200 mM KCl |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.92 | 57.86 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 67.41 | α = 90 |
| b = 67.41 | β = 90 |
| c = 179.791 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 65 2 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 295 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2019-10-15 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 295 | SCINTILLATION | ORNL ANGER CAMERA | | 2019-09-11 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.542 | | |
| 2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.00-4.16 | ORNL Spallation Neutron Source | MANDI |
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 | 1.63 | 48.96 | 99.8 | | | | | 0.991 | | 21.4 | 6.7 | | 31092 | | | 25.62 |
| 2 | 2.15 | 14.82 | 88.6 | | | | | 0.95 | | 9.7 | 9.4 | | 12347 | | | 25.62 |
| 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 | 1.63 | 1.66 | | | | | | 0.833 | | | | |
| 2 | 2.15 | 2.23 | | | | | | 0.49 | | | | |
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 | 1.63 | 33.13 | | 1.35 | | 31054 | 1580 | 99.61 | | 0.1345 | 0.1334 | 0.1354 | 0.1548 | 0.1583 | | 43.07 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.15 | 14.09 | | | | 12346 | | 88.03 | | | 0.2318 | | 0.2813 | | | |
| 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 | 20.647 |
| f_dihedral_angle_d | 20.647 |
| f_angle_d | 1.462 |
| f_angle_d | 1.462 |
| f_chiral_restr | 0.078 |
| f_chiral_restr | 0.078 |
| f_bond_d | 0.011 |
| f_bond_d | 0.011 |
| f_plane_restr | 0.008 |
| f_plane_restr | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1420 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 129 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
