1VJN
Crystal structure of a putative zn-dependent hydrolase of the metallo-beta-lactamase superfamily (tm0207) from thermotoga maritima at 2.00 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 5 | 277 | 20% PEG-6000, 0.1M citric acid pH 5.0, 1M LiCl, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.16 | 49.9 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 43.147 | α = 73.66 |
| b = 45.723 | β = 89.25 |
| c = 63.491 | γ = 64.96 |
| Symmetry | |
|---|---|
| Space Group | P 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 | APS-1 | water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror | 2002-10-26 | M | MAD | |||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2002-12-02 | M | MAD | ||||||
| 1,2 | 1 | |||||||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-BM | APS | 19-BM | |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.979148, 0.898403 | SSRL | BL9-1 |
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 | 2 | 50 | 93.6 | 0.079 | 10.38 | 2.48 | 26349 | 40.21 | |||||||||||
| 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 | 2 | 2.07 | 73.47 | 0.441 | 2.03 | 2.19 | 2099 | ||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 2 | 38.91 | 25012 | 1319 | 93.38 | 0.18053 | 0.1784 | 0.21993 | RANDOM | 25.677 | |||||||
| 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] | |
| 0.97 | 0.19 | 0.97 | -0.92 | 0.75 | -0.66 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.86 |
| r_dihedral_angle_3_deg | 14.217 |
| r_dihedral_angle_4_deg | 11.889 |
| r_scangle_it | 8.672 |
| r_dihedral_angle_1_deg | 6.189 |
| r_scbond_it | 5.902 |
| r_mcangle_it | 3.821 |
| r_mcbond_it | 2.785 |
| r_angle_refined_deg | 1.458 |
| r_angle_other_deg | 0.754 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2966 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 154 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALEPACK | data scaling |
| SOLVE | phasing |
| RESOLVE | model building |
| REFMAC | refinement |
| RESOLVE | phasing |
