Neutron Structure of PcyA D105N 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 | 3F0M | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 293 | NaCl, ammonium sulfate, MES |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.74 | 55.13 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 71.174 | α = 90 |
| b = 97.523 | β = 90 |
| c = 43.277 | 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 2M | | 2021-06-06 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 300 | DIFFRACTOMETER | iBIX | | 2021-03-20 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0 | Photon Factory | AR-NW12A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.63-6.06 | JPARC MLF | BL-03 |
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 | 1.38 | 43.28 | 99.6 | | | | | 0.997 | | 12.2 | 4.9 | | 62402 | | | 15.07 |
| 2 | 2.1 | 21.16 | 99.3 | | | | | 0.9828 | | 9.18 | 6.9377 | | 18158 | | | 15.07 |
| 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 | 1.38 | 1.4 | | | | | | 0.752 | | | | |
| 2 | 2.1 | 2.17 | | | | | | 0.4789 | | | | |
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 | 1.38 | 34.58 | | 1.35 | | 62359 | 1127 | 99.34 | | 0.1505 | 0.1501 | 0.15 | 0.1716 | 0.17 | | 17.93 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.1 | 21.12 | | | | 18158 | | 98.6847 | | | 0.1657 | | 0.1806 | | | |
| 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 | 19.4914 |
| f_angle_d | 1.4608 |
| f_chiral_restr | 0.0921 |
| f_bond_d | 0.016 |
| f_plane_restr | 0.0117 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1925 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 219 |
| Heterogen Atoms | 44 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| REFMAC | phasing |
