Neutron Structure of PcyA I86D Mutant Complexed with Biliverdin at Room Temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5B4H | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 293 | ammonium sulfate, sodium chloride, sodium cacodylate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.66 | 53.77 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 71.325 | α = 90 |
| b = 97.415 | β = 90 |
| c = 43.134 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 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 | 300 | PIXEL | DECTRIS PILATUS3 S 2M | | 2017-12-05 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 300 | IMAGE PLATE | BIODIFF | | 2017-08-30 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98 | Photon Factory | BL-17A |
| 2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 3.1 | FRM II | BIODIFF |
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 | 1.9 | 50 | 100 | | | | | 0.988 | | 18.714 | 4.9 | | 24473 | | | 26.18 |
| 2 | 2 | 55 | 84.2 | | | | | 0.9675 | | 6.532 | 1.9 | | 17734 | | | 26.18 |
| 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 | 1.9 | 1.93 | | | | | | 0.797 | | | | |
| 2 | 2 | 2.05 | | | | | | 0.762 | | | | |
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 | 1.9 | 36.91 | | 1.35 | | 24427 | 1999 | 99.74 | | 0.1408 | 0.1378 | 0.14 | 0.1741 | 0.17 | | 19.21 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 29.55 | | | | 17648 | | 84.1 | | | 0.1706 | | 0.2029 | | | |
| 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 | 28.8209 |
| f_angle_d | 1.4559 |
| f_chiral_restr | 0.0729 |
| f_bond_d | 0.016 |
| f_plane_restr | 0.0129 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1934 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 159 |
| Heterogen Atoms | 43 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
