3H5N
Crystal structure of E. coli MccB + ATP
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3H5A | PDB entry 3H5A |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291.2 | 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 25 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.96 | 37.32 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 55.847 | ¦Á = 90 |
| b = 138.239 | ¦Â = 92.62 |
| c = 80.224 | ¦Ã = 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 | IMAGE PLATE | MAR scanner 300 mm plate | Rosenbaum-Rock vertical focusing mirror | 2007-12-02 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97926 | APS | 22-ID |
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 | 1.85 | 50 | 92.9 | 0.054 | 19.166 | 3.1 | 96263 | 96263 | 24.9 | ||||||||||
| 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) | |||||||||||
| 1.85 | 1.92 | 89 | 0.364 | 2.8 | 9202 | ||||||||||||||
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 | PDB entry 3H5A | 1.9 | 42.64 | 88775 | 4421 | 93.01 | 0.207 | 0.204 | 0.256 | RANDOM | 22.839 | ||||||
| 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] | |
| 0.28 | -0.15 | -0.43 | 0.14 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.707 |
| r_dihedral_angle_4_deg | 21.183 |
| r_dihedral_angle_3_deg | 15.052 |
| r_dihedral_angle_1_deg | 6.15 |
| r_scangle_it | 2.852 |
| r_scbond_it | 2.021 |
| r_angle_refined_deg | 1.323 |
| r_mcangle_it | 1.129 |
| r_mcbond_it | 0.909 |
| r_nbtor_refined | 0.308 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10428 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 731 |
| Heterogen Atoms | 137 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| X-GEN | data scaling |
| HKL-2000 | data reduction |
| REFMAC | phasing |
