5Y8R
ZsYellow at pH 3.5
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2OGR | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 295.5 | Na-citrate, NaCl | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.14 | 60.86 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 111.178 | α = 90 |
| b = 111.178 | β = 90 |
| c = 103.751 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 41 2 2 |
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 210 | 2016-11-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.9795 | PAL/PLS | 7A (6B, 6C1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.3 | 20 | 94.3 | 39.421 | 7 | 13860 | |||||||||||||
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2OGR | 2.3 | 19.16 | 13171 | 662 | 93.83 | 0.208 | 0.2056 | 0.2575 | RANDOM | 68.36 | ||||||
| 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] | |
| -2.2 | -2.2 | 4.4 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.596 |
| r_dihedral_angle_4_deg | 22.513 |
| r_dihedral_angle_3_deg | 17.561 |
| r_dihedral_angle_1_deg | 8.09 |
| r_angle_refined_deg | 1.981 |
| r_angle_other_deg | 0.833 |
| r_chiral_restr | 0.112 |
| r_bond_refined_d | 0.016 |
| r_gen_planes_refined | 0.009 |
| r_gen_planes_other | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1790 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 21 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| HKL-2000 | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
