3MBD
Crystal structure of fructose bisphosphate aldolase from Encephalitozoon cuniculi, bound to phosphate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | 90% PACT SCREEN CONDITION F10, 10% ADDITIVE SCREEN G12: 90MM BIS-TRIS PROPANE PH 6.5, 18% PEG 3350, 18 MM NAKHPO4, 10 MM UREA, PROTEIN AT 24.7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.41 | 63.95 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.96 | α = 90 |
| b = 137.61 | β = 90 |
| c = 62.23 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2010-03-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
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 | 2 | 36.8 | 99.8 | 0.056 | 21.83 | 6.2 | 35792 | 35720 | -3 | ||||||||||
| 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 | 2 | 2.05 | 99.3 | 0.489 | 3.6 | 6.1 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1QO5 | 2 | 35.34 | 35792 | 33882 | 1749 | 99.58 | 0.16375 | 0.1624 | 0.19021 | RANDOM | 29.39 | |||||
| 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] | |
| -0.54 | -0.98 | 1.52 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.385 |
| r_dihedral_angle_4_deg | 22.125 |
| r_dihedral_angle_3_deg | 13.748 |
| r_dihedral_angle_1_deg | 5.804 |
| r_scangle_it | 3.645 |
| r_scbond_it | 2.234 |
| r_angle_refined_deg | 1.395 |
| r_mcangle_it | 1.371 |
| r_angle_other_deg | 0.913 |
| r_mcbond_it | 0.763 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2631 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 192 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
