X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2AYH | PDB ENTRY 2AYH |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 9 | HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) PEG 8000 AND 8% (BY VOL.) ETHYLENE GLYCOL., vapor diffusion - hanging drop | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.3 | 46.5 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 44.95 | α = 92.6 |
| b = 46.55 | β = 109.28 |
| c = 63.99 | γ = 116.68 |
| Symmetry | |
|---|---|
| Space Group | P 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 294 | IMAGE PLATE | MARRESEARCH | MIRRORS | 1995-01-05 | M | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU FR-D | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.07 | 29.62 | 93.5 | 0.109 | 0.109 | 2.94 | 1.8 | 24275 | 20.94 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 2.07 | 2.15 | 90 | 0.196 | 0.19 | 3.3 | 1.8 | |||||||||||||
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-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2AYH | 2.07 | 9.99 | 24053 | 2381 | 93.5 | 0.176 | 0.16 | 0.235 | 0.21 | RANDOM | 20.8 | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| p_staggered_tor | 16.3 |
| p_planar_tor | 4.9 |
| p_scangle_it | 3.447 |
| p_mcangle_it | 3.067 |
| p_scbond_it | 2.403 |
| p_mcbond_it | 2.196 |
| p_chiral_restr | 0.137 |
| p_planar_d | 0.034 |
| p_angle_d | 0.033 |
| p_bond_d | 0.013 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3376 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 244 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALA | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
| CCP4 | data scaling |














