3FJP
Apo structure of Biotin protein ligase from Aquifex aeolicus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WPY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 0.1M MES, 0.2M AMMONIUM SULPHATE, 15% MPEG 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.37 | 48.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.533 | α = 90 |
b = 61.342 | β = 90.49 |
c = 73.283 | 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 225 mm CCD | mirrors | 2006-09-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SRS BEAMLINE PX10.1 | 0.968 | SRS | PX10.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 31.47 | 92.4 | 0.035 | 22.4 | 4.5 | 20759 | 2 | 49.21 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.3 | 2.42 | 64.6 | 0.308 | 5 | 4.3 | 2066 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | 1WPY | 2.3 | 30.867 | 1.42 | 20745 | 1055 | 92.34 | 0.2229 | 0.22 | 0.2793 | RANDOM | 50.6 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.767 |
f_angle_d | 1.368 |
f_chiral_restr | 0.083 |
f_bond_d | 0.012 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3557 |
Nucleic Acid Atoms | |
Solvent Atoms | 59 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
PHASER | phasing |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |