3K6U
M. acetivorans Molybdate-Binding Protein (ModA) in Unliganded Open Form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 293 | 1.4M tri-Ammonium Citrate, p6.4, vapor diffusion, sitting drop, temperature 293K |
2 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 293 | 1.6M tri-Ammonium Citrate, p6.4, soaked in 0.5M potassium iodide for 30 seconds, vapor diffusion, sitting drop, temperature 293K |
3 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 293 | 1.6M tri-Ammonium Citrate, p6.4, soaked in 1M cesium chloride for 18 minutes, vapor diffusion, sitting drop, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.179 | α = 90 |
b = 82.179 | β = 90 |
c = 104.94 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 315 | 2004-11-21 | SINGLE WAVELENGTH | |||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2004-11-21 | SINGLE WAVELENGTH | |||||||
3 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2004-11-23 | SINGLE WAVELENGTH | |||||||
1,2,3 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.954 | ALS | 8.2.2 |
2 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 1.459 | ALS | 8.2.2 |
3 | ROTATING ANODE | OTHER | 1.542 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||
1,2,3 | 1.94 | 38.26 | 99.9 | 0.092 | 0.079 | 18.6 | 10.86 | 29447 |
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) | ||||||||||
1,2,3 | 1.94 | 2.01 | 100 | 0.5 | 0.468 | 10.43 | 2936 |
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 | MIRAS | THROUGHOUT | 1.95 | 38.26 | 29271 | 1453 | 99.94 | 0.178 | 0.177 | 0.208 | RANDOM | 17.613 |
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] | |
0.93 | 0.46 | 0.93 | -1.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.176 |
r_dihedral_angle_4_deg | 21.826 |
r_dihedral_angle_3_deg | 13.497 |
r_dihedral_angle_1_deg | 5.982 |
r_scangle_it | 4.318 |
r_scbond_it | 2.613 |
r_mcangle_it | 1.64 |
r_angle_refined_deg | 1.392 |
r_mcbond_it | 0.883 |
r_chiral_restr | 0.108 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2423 |
Nucleic Acid Atoms | |
Solvent Atoms | 176 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MLPHARE | phasing |
DM | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |