4MLZ
Crystal structure of periplasmic binding protein from Jonesia denitrificans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 289 | 0.2M CaCl2, 0.1M Tris, 25% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.678 | α = 90 |
b = 72.741 | β = 101.32 |
c = 71.306 | 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 210r | 2012-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.97927 | APS | 19-BM |
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 | 1.72 | 50 | 99.9 | 0.107 | 19.9 | 4.6 | 63028 | 62981 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.73 | 1.76 | 99.3 | 0.581 | 2.09 | 3.3 | 3151 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.72 | 35.8 | 62314 | 62314 | 3158 | 98.69 | 0.138 | 0.138 | 0.1351 | 0.193 | RANDOM | 18.5384 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.88 | -0.37 | -0.83 | 1.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.232 |
r_sphericity_free | 30.665 |
r_dihedral_angle_3_deg | 10.866 |
r_dihedral_angle_4_deg | 10.616 |
r_sphericity_bonded | 10.064 |
r_dihedral_angle_1_deg | 5.042 |
r_rigid_bond_restr | 2.216 |
r_angle_refined_deg | 1.301 |
r_angle_other_deg | 0.772 |
r_chiral_restr | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4456 |
Nucleic Acid Atoms | |
Solvent Atoms | 603 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |
MLPHARE | phasing |
DM | phasing |
SHELXDE | phasing |
ARP/wARP | model building |
RESOLVE | phasing |
Coot | model building |