5FYR
Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, myoinositol complex
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 10 | PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.99 | 38.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 135.443 | α = 90 |
| b = 135.443 | β = 90 |
| c = 113.732 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 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 | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-05-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.45 | 48.93 | 99.7 | 0.07 | 14.5 | 7.2 | 184175 | 2 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.45 | 1.47 | 95.2 | 0.6 | 2.5 | 5.7 | |||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 5FYP | 1.45 | 48.93 | 174938 | 9159 | 99.68 | 0.14722 | 0.14488 | 0.19184 | RANDOM | 16.818 | ||||||
| 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] | |
| -0.07 | -0.07 | 0.15 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.774 |
| r_sphericity_free | 27.31 |
| r_dihedral_angle_4_deg | 16.4 |
| r_dihedral_angle_3_deg | 11.608 |
| r_sphericity_bonded | 9.027 |
| r_dihedral_angle_1_deg | 6.327 |
| r_rigid_bond_restr | 4.143 |
| r_long_range_B_refined | 3.962 |
| r_long_range_B_other | 3.925 |
| r_scangle_other | 3.216 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9065 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1072 |
| Heterogen Atoms | 67 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
