Neutron Structure of Compound II of Ascorbate Peroxidase
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2XIF | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 300 | 2.25 M Lithium sulfate, 0.1 M HEPES pH 8.3 - 8.9 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.23 | 44.91 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 82.095 | α = 90 |
| b = 82.095 | β = 90 |
| c = 75.162 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 42 21 2 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 100 | IMAGE PLATE | MAATEL IMAGINE | multilayer | 2015-10-14 | L | LAUE |
| 2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | multilayer | 2015-10-20 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 3.2 - 4.2 | ILL | LADI III |
| 2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | | |
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 | 2.2 | 40 | 69.8 | 0.18 | | | | | | 7 | 4 | | 9220 | | | |
| 2 | 1.8 | 19.91 | 98.72 | 0.16 | | | | | | 9.4 | 6.8 | | 23857 | | | |
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 | 1.806 | 19.91 | | 1.36 | | 23857 | 1194 | 98.72 | | 0.1578 | 0.1547 | 0.1513 | 0.2159 | 0.2128 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.202 | 36.714 | | 2.03 | | 9220 | 462 | 68.14 | | 0.2401 | 0.2364 | | 0.3104 | | | |
| 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] |
|---|
| 0.4889 | | | 0.4889 | | -0.9778 |
| 0.4889 | | | 0.4889 | | -0.9778 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 11.898 |
| f_dihedral_angle_d | 11.898 |
| f_angle_d | 1.366 |
| f_angle_d | 1.366 |
| f_chiral_restr | 0.115 |
| f_chiral_restr | 0.115 |
| f_bond_d | 0.016 |
| f_bond_d | 0.016 |
| f_plane_restr | 0.009 |
| f_plane_restr | 0.009 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1899 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 390 |
| Heterogen Atoms | 54 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
