1ZEX
CCG A-DNA
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 160D | ndb entry ADJ049 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 298 | Na Cacodylate, CaCl2, Spermine, MPD in resevoir, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.9 | 33.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 23.956 | α = 90 |
| b = 45.133 | β = 90 |
| c = 44.933 | 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 | 103 | IMAGE PLATE | RIGAKU RAXIS IV | 2003-10-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RUH3R | |||
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 | 1.65 | 99 | 93.8 | 0.049 | 16 | 5906 | 2 | ||||||||||||
| 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) | |||||||||||
| 1.65 | 1.71 | 76.8 | 0.15 | 4.72 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | ndb entry ADJ049 | 1.65 | 16.39 | 2 | 5137 | 622 | 100 | 0.248 | 0.24 | 0.25 | 0.25 | 0.25 | RANDOM | 7.18 | |||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[3][3] | |||||
| 0.37 | -0.37 | |||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_angle_refined_deg | 1.292 |
| r_scangle_it | 1.104 |
| r_scbond_it | 0.713 |
| r_nbtor_refined | 0.268 |
| r_symmetry_vdw_refined | 0.242 |
| r_xyhbond_nbd_refined | 0.231 |
| r_symmetry_hbond_refined | 0.192 |
| r_nbd_refined | 0.188 |
| r_chiral_restr | 0.055 |
| r_bond_refined_d | 0.006 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 404 |
| Solvent Atoms | 51 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| EPMR | phasing |
