4PLU
Crystal structure of Macrophage Migration Inhibitory Factor in complex with benzaldehyde
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | 2 M ammonium Sulphate, 3% 2-propanol,20 mM Tris.HCl pH 7.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.73 | 54.96 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 67.601 | ¦Á = 90 |
| b = 67.812 | ¦Â = 90 |
| c = 88.323 | ¦Ã = 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 | x-ray | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2013-11-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
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 | 1.63 | 50 | 98.7 | 0.029 | 26.5 | 4.7 | 50847 | ||||||||||||
| 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 | 1.63 | 1.66 | 97.6 | 0.214 | 4.5 | 2481 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.63 | 42.09 | 50787 | 2581 | 98.69 | 0.1842 | 0.1825 | 0.2136 | RANDOM | 15.132 | |||||||
| 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] | |
| 0.01 | -0.01 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.614 |
| r_dihedral_angle_4_deg | 17.054 |
| r_dihedral_angle_3_deg | 9.418 |
| r_dihedral_angle_1_deg | 5.989 |
| r_angle_other_deg | 4.71 |
| r_mcangle_it | 2.088 |
| r_angle_refined_deg | 2.087 |
| r_mcbond_it | 1.538 |
| r_mcbond_other | 1.538 |
| r_chiral_restr | 0.124 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2522 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 354 |
| Heterogen Atoms | 46 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data reduction |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data scaling |
| PHASER | phasing |
| DENZO | data reduction |
| SCALEPACK | data scaling |
