Neutron and X-ray joint refined structure of PcCel45A apo form at 298K.
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | 60% 3-methyl-1,5-pentanediol, 50 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.41 | 48.96 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 46.152 | α = 90 |
| b = 59.067 | β = 90 |
| c = 64.285 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 298 | STORAGE PHOSPHORS | IBIX (BL03), J-PARC | | 2014-04-25 | L | LAUE |
| 2 | 1 | x-ray | 298 | CCD | ADSC QUANTUM 315r | | 2014-06-09 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.5-5.4 | JPARC MLF | BL-03 |
| 2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.0 | Photon Factory | BL-5A |
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 | 1.5 | 20.4 | 93.3 | 0.245 | | | | | | 3.9 | 3.9 | | 25581 | | | |
| 2 | 1 | 50 | 99.5 | 0.08 | | | | | | 106 | 13.1 | | 99189 | | | |
| 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 | 1.5 | 1.55 | | 0.501 | | | | | | 1.4 | 2.1 | |
| 2 | 1 | 1.02 | | 0.299 | | | | | | 6.5 | 6.3 | |
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 |
|---|
| NEUTRON DIFFRACTION | | 1.5 | 18.826 | | | | 25433 | 2548 | 94.22 | | 0.2298 | 0.2275 | | 0.2506 | | | |
| X-RAY DIFFRACTION | | 1 | 28.233 | | 1.49 | | 94159 | 9389 | 99.26 | | 0.1367 | 0.1349 | 0.1342 | 0.1531 | 0.1524 | | 27.4849 |
| 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 | 16.335 |
| f_angle_d | 1.208 |
| f_chiral_restr | 0.088 |
| f_bond_d | 0.008 |
| f_plane_restr | 0.006 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1261 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 152 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| STARGazer | data reduction |
| STARGazer | data scaling |
