8FBG
Crystal structure of NSD1 Mutant-Y1869C
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3OOI | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291 | 20% p3350, 0.2M KCl | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.12 | 41.96 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.449 | α = 90 |
| b = 64.947 | β = 93.17 |
| c = 81.408 | γ = 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 | RIGAKU SATURN A200 | 2021-06-12 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU FR-E | 1.54 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.29 | 50 | 96.7 | 0.113 | 0.128 | 0.061 | 10.8 | 4.1 | 19253 | 38.79 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.3 | 2.34 | 96.8 | 0.771 | 0.881 | 0.419 | 0.897 | 4 | |||||||||||
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 | 3OOI | 2.29 | 27.09 | 19076 | 899 | 95.7 | 0.217 | 0.214 | 0.271 | RANDOM | 29.58 | ||||||
| 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] | |
| -3.423 | 1.9521 | 3.9716 | -0.5486 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_other_torsion | 17.94 |
| t_omega_torsion | 3.15 |
| t_angle_deg | 1.09 |
| t_bond_d | 0.01 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3320 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 173 |
| Heterogen Atoms | 65 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALEPACK | data scaling |
| PHASER | phasing |
| BUSTER | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
