3C1L
Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277 | NANODROP, 20.0% PEG 6000, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP | 6.2 | 277 | NANODROP, 0.2M NaCl, 50.0% PEG 200, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.69 | α = 90 |
b = 68.06 | β = 95.94 |
c = 266.83 | 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 | MARMOSAIC 325 mm CCD | Flat mirror (vertical focusing) | 2007-02-11 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Adjustable focusing mirrors in K-B geometry | 2007-08-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837 | SSRL | BL11-1 |
2 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97942 | APS | 23-ID-D |
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 | 29.814 | 84.6 | 0.058 | 7.38 | 138837 | -3 | 21.909 |
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 | 41.9 | 0.354 | 1.6 |
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 | SAD + MOLECULAR REPLACEMENT | THROUGHOUT | 2 | 29.814 | 138822 | 6959 | 87.53 | 0.174 | 0.171 | 0.225 | RANDOM | 24.95 |
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] | |
-0.31 | -0.04 | 0.25 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.995 |
r_dihedral_angle_3_deg | 15.072 |
r_dihedral_angle_4_deg | 13.86 |
r_scangle_it | 5.879 |
r_dihedral_angle_1_deg | 5.846 |
r_scbond_it | 4.223 |
r_mcangle_it | 2.248 |
r_angle_refined_deg | 1.498 |
r_mcbond_it | 1.466 |
r_angle_other_deg | 0.992 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 16600 |
Nucleic Acid Atoms | |
Solvent Atoms | 731 |
Heterogen Atoms | 176 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
MolProbity | model building |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
XDS | data reduction |
MOSFLM | data reduction |
XSCALE | data scaling |
SCALA | data scaling |
SHARP | phasing |
MOLREP | phasing |