7AP5
Crystal structure of phycoerythrin from cyanobacterium Nostoc sp. WR13 contains multiple stacks of hexameric assemblies which resemble the rods of phycobilisome.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5NB4 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 294.15 | Morpheus screen condition C9: 10% w/v PEG 20 000, 20% v/v PEG MME 550 precipitants; 0.03 M NPS (Nitrate, Phosphate & Sulfate) mix of additives; 0.01 M bicine/Trizma base pH 8.5 buffer system | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.94 | 58.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 192.759 | α = 90 |
| b = 192.759 | β = 90 |
| c = 524.486 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2018-09-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97950 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.13 | 159.07 | 95.6 | 0.283 | 0.298 | 0.093 | 0.996 | 8 | 10.2 | 156067 | 29.7 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.133 | 2.322 | 80.1 | 1.653 | 1.749 | 0.567 | 0.622 | 1.6 | 9.3 | ||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5NB4 | 2.131 | 49.005 | 156062 | 7765 | 75.005 | 0.18 | 0.1774 | 0.225 | 40.685 | |||||||
| 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] | |
| -0.09 | -0.045 | -0.09 | 0.291 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.412 |
| r_dihedral_angle_4_deg | 18.323 |
| r_dihedral_angle_3_deg | 14.236 |
| r_dihedral_angle_other_3_deg | 9.212 |
| r_lrange_it | 6.056 |
| r_lrange_other | 6.013 |
| r_dihedral_angle_1_deg | 5.33 |
| r_scangle_other | 4.066 |
| r_scangle_it | 4.064 |
| r_mcangle_other | 3.125 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 20592 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1365 |
| Heterogen Atoms | 4153 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data processing |
| pointless | data scaling |
| Aimless | data scaling |
| STARANISO | data scaling |
| PHASER | phasing |
| XDS | data reduction |
