3F3K
The structure of uncharacterized protein YKR043C from Saccharomyces cerevisiae.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 0.2M Li3Citrate, 16% PEG 3350, 4%MPD, 10% Glycerol, Trypsin 1/10, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.98 | 58.66 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 84.037 | α = 90 |
| b = 86.277 | β = 90 |
| c = 100.168 | 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 QUANTUM 315 | 2008-06-29 | M | MAD | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97948,0.97931 | APS | 19-ID |
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 | 1.75 | 50 | 98.2 | 0.074 | 40.5 | 9.9 | 72754 | 72754 | -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 | 1.75 | 1.78 | 98.4 | 0.265 | 8.9 | 3587 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 1.75 | 43.15 | 72653 | 72653 | 3660 | 98.14 | 0.143 | 0.143 | 0.141 | 0.17 | RANDOM | 15.734 | |||||
| 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] | |
| -0.61 | 0.5 | 0.11 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.947 |
| r_dihedral_angle_4_deg | 16.363 |
| r_dihedral_angle_3_deg | 11.951 |
| r_dihedral_angle_1_deg | 6.099 |
| r_scangle_it | 3.802 |
| r_scbond_it | 2.276 |
| r_angle_refined_deg | 1.346 |
| r_mcangle_it | 1.334 |
| r_angle_other_deg | 0.882 |
| r_mcbond_it | 0.721 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4217 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 939 |
| Heterogen Atoms | 36 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
