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 | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.16 | 49.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 43.147 | α = 73.66 |
b = 45.723 | β = 89.25 |
c = 63.491 | γ = 64.96 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||||||||||||||||
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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 | |
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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 | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2966 |
Nucleic Acid Atoms | |
Solvent Atoms | 154 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | model building |
REFMAC | refinement |
RESOLVE | phasing |