3SGL
The crystal structure of MnmC from Yersinia pestis bound with FAD and SAM
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 310 | 0.1M HEPES PH 7.0 30% (v/v) Jeffamine ED-2001 PH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 310K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.47 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.085 | α = 90 |
b = 59.815 | β = 100.18 |
c = 100.797 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 315r | 2010-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9790 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.7 | 50 | 100 | 0.143 | 0.177 | 9.3 | 5.1 | 21571 | 21571 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.7 | 2.75 | 100 | 0.734 | 0.819 | 2.1 | 5.2 |
Refinement
Statistics | |||||||||||||||||||
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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 3PVC | 2.7 | 50 | 18983 | 1022 | 92.68 | 0.18413 | 0.1801 | 0.25933 | RANDOM | 25.751 |
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] | |
-0.2 | -0.3 | 0.51 | -0.41 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.37 |
r_dihedral_angle_3_deg | 18.607 |
r_dihedral_angle_4_deg | 18.183 |
r_dihedral_angle_1_deg | 5.746 |
r_scangle_it | 4.774 |
r_scbond_it | 2.942 |
r_mcangle_it | 1.712 |
r_angle_refined_deg | 1.491 |
r_mcbond_it | 0.868 |
r_chiral_restr | 0.093 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4916 |
Nucleic Acid Atoms | |
Solvent Atoms | 91 |
Heterogen Atoms | 81 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |