2QEC
Crystal structure of histone acetyltransferase HPA2 and related acetyltransferase (NP_600742.1) from Corynebacterium glutamicum ATCC 13032 at 1.90 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277 | NANODROP, 8.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| 2 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | NANODROP, 0.2M Li2SO4, 40.0% PEG 400, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 79.07 | α = 90 |
| b = 79.07 | β = 90 |
| c = 181.26 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-01-18 | M | SINGLE WAVELENGTH | |||||
| 2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-01-07 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91162 | SSRL | BL11-1 |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97917, 0.91837, 0.97886 | SSRL | BL11-1 |
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 | ||||||||
| 1,2 | 1.9 | 27.64 | 99.5 | 0.071 | 17.36 | 17.62 | 27197 | 32.59 | |||||||||||
| 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) | |||||||||||
| 1,2 | 1.9 | 1.97 | 99.3 | 0.905 | 2 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MAD, MOLECULAR REPLACEMENT | THROUGHOUT | 1.9 | 27.64 | 27120 | 1363 | 99.48 | 0.195 | 0.195 | 0.193 | 0.242 | RANDOM | 41.353 | ||||||
| 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] | |
| 1.77 | 0.89 | 1.77 | -2.66 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.366 |
| r_dihedral_angle_4_deg | 15.97 |
| r_dihedral_angle_3_deg | 12.391 |
| r_scangle_it | 7.142 |
| r_dihedral_angle_1_deg | 6.529 |
| r_scbond_it | 5.4 |
| r_mcangle_it | 3.613 |
| r_mcbond_it | 2.37 |
| r_angle_refined_deg | 1.609 |
| r_angle_other_deg | 1.095 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1375 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 151 |
| Heterogen Atoms | 36 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MolProbity | model building |
| REFMAC | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
| XDS | data reduction |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHELXD | phasing |
| autoSHARP | phasing |
| PHASER | phasing |
