X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2BR9 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8 | 289.15 | 0.1 M Imidazole pH 8.0, 10 % PEG 4000, 30 % MPD |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.35 | 47.66 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 77.88 | α = 90 |
| b = 81.04 | β = 90 |
| c = 83.28 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 2 2 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 | MARMOSAIC 225 mm CCD | 2020-03-12 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | RRCAT INDUS-2 BEAMLINE PX-BL21 | 0.97947 | RRCAT INDUS-2 | PX-BL21 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.85 | 36.46 | 99.4 | 0.12 | 0.12 | 0.131 | 0.052 | 0.994 | 9.8 | 6.2 | 22570 | 19.4 | |||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 1.85 | 1.95 | 98.1 | 0.743 | 0.743 | 0.815 | 0.33 | 0.773 | 2.6 | 5.8 | |||||||||
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-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 | 2BR9 | 1.85 | 36.46 | 21400 | 1149 | 99.28 | 0.16763 | 0.16653 | 0.17 | 0.18879 | 0.19 | RANDOM | 24.092 | ||||
| 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] | |
| -1.56 | -0.57 | 2.13 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.087 |
| r_dihedral_angle_4_deg | 18.549 |
| r_dihedral_angle_3_deg | 13.625 |
| r_long_range_B_refined | 7.014 |
| r_long_range_B_other | 7.013 |
| r_scangle_other | 5.541 |
| r_dihedral_angle_1_deg | 5.303 |
| r_scbond_it | 3.662 |
| r_scbond_other | 3.661 |
| r_mcangle_other | 2.983 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1957 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 161 |
| Heterogen Atoms | 25 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
