1XMT
X-ray structure of gene product from arabidopsis thaliana at1g77540
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | PROTEIN 10 MG/ML, 29% MEPEG 5K, 0.100 M SODIUM CITRATE, 0.100 M PIPES, CRYOPROTRECTED CRYSTAL SOAKED IN 1 M SODIUM BROMIDE FOR CIRCA 40 SECONDS, pH 6.5, Vapor diffusion, hanging drop, temperature 277 KK |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.08 | 40.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 27.349 | ¦Á = 90 |
| b = 60.601 | ¦Â = 91.5 |
| c = 29.424 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 | MAR CCD 165 mm | RH MIRROR | 2004-08-08 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 32-ID | 0.926676, 0.926676, 0.919801, 0.919528, 0.91302 | APS | 32-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 | 1.15 | 20.29 | 95.9 | 0.039 | 16.5 | 3.5 | 32713 | ||||||||||||
| 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) | |||||||||||
| 1.15 | 1.18 | 70.7 | 0.345 | 2.22 | 1.9 | ||||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MAD (BROMIDE PHASING) | THROUGHOUT | 1.15 | 30.303 | 31030 | 1658 | 95.95 | 0.149 | 0.149 | 0.1476 | 0.1703 | RANDOM | 17.748 | ||||||
| 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] | |
| -0.306 | 0.031 | 0.039 | 0.269 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| Sphericity. Free atoms | 6.792 |
| r_scangle_it | 6.788 |
| Sphericity. Bonded atoms | 6.321 |
| r_dihedral_angle_1_deg | 5.835 |
| r_scbond_it | 4.668 |
| r_mcangle_it | 3.96 |
| r_mcbond_it | 2.75 |
| Rigid bond restraints | 2.382 |
| r_angle_refined_deg | 2.022 |
| r_nbtor_refined | 0.326 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 805 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 125 |
| Heterogen Atoms | 11 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
| CNS | refinement |
| REFMAC | refinement |
| PHENIX | phasing |
| ARP/wARP | model building |
