2IX1
RNase II D209N mutant
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | VAPOUR DIFFUSION IN SITTING DROPS WITH 1.5 MICRO-L OF PROTEIN SOLUTION, 20 MM TRIS-HCL PH 8, 150 MM NACL, 10% GLYCEROL AND 1 MM DTT, AND 1.5 MICRO-L OF WELL SOLUTION,2.4 M SODIUM MALONATE PH 6.0, AT 293 K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.29 | 71.3 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 86.316 | α = 90 |
| b = 86.316 | β = 90 |
| c = 279.245 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 |
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 | 2004-11-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 | |
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 | 2.74 | 51 | 99.9 | 0.08 | 28.6 | 9.2 | 30737 | ||||||||||||
| 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 | 2.74 | 2.85 | 100 | 0.64 | 3.4 | ||||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MIRAS | THROUGHOUT | 2.74 | 29.3 | 29091 | 1547 | 99.9 | 0.187 | 0.185 | 0.18 | 0.225 | 0.22 | RANDOM | 54.83 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| -0.06 | -0.03 | -0.06 | 0.09 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 35.052 |
| r_dihedral_angle_3_deg | 20.332 |
| r_dihedral_angle_4_deg | 19.713 |
| r_scangle_it | 7.574 |
| r_dihedral_angle_1_deg | 6.408 |
| r_scbond_it | 4.874 |
| r_mcangle_it | 3.396 |
| r_mcbond_it | 2.003 |
| r_angle_refined_deg | 1.428 |
| r_nbtor_refined | 0.313 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5092 |
| Nucleic Acid Atoms | 287 |
| Solvent Atoms | 48 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SHARP | model building |
| SCALEPACK | data scaling |
| SHELXCD | phasing |
| SHELXD | phasing |
| SHELXE | phasing |
| SHARP | phasing |
| REFMAC | refinement |
