Crystal structure of the RRM domain of mouse Deleted in azoospermia-like in complex with RNA, UUGUUCUU
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 10 MM MAGNESIUM FORMATE, 20 % (W/V) PEG 3350, 0.1 MM ZINC ACETATE | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.73 | 55 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 38.1 | α = 90 |
| b = 52.06 | β = 90 |
| c = 60.49 | 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 | x-ray | 100 | CCD | ADSC CCD | KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING | 2010-04-14 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | 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 | 1.35 | 27.41 | 96 | 0.06 | 15 | 5.4 | 26034 | 6 | 16.33 | ||||||||||
| 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 | 1.35 | 1.42 | 87.3 | 0.65 | 2.4 | 5.1 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | NONE | 1.35 | 27.41 | 24721 | 1313 | 96.05 | 0.16292 | 0.16131 | 0.16 | 0.19267 | 0.19 | RANDOM | 19.382 | ||||
| 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] | |
| -0.08 | 0.23 | -0.16 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.729 |
| r_dihedral_angle_4_deg | 26.313 |
| r_dihedral_angle_3_deg | 10.858 |
| r_dihedral_angle_1_deg | 6.297 |
| r_scangle_it | 5.342 |
| r_scbond_it | 3.807 |
| r_mcangle_it | 2.864 |
| r_rigid_bond_restr | 1.971 |
| r_mcbond_it | 1.83 |
| r_angle_refined_deg | 1.642 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 679 |
| Nucleic Acid Atoms | 124 |
| Solvent Atoms | 129 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHELX | phasing |
