1K53
Monomeric Protein L B1 Domain with a G15A Mutation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HZ5 | pdb entry 1HZ5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 225mM ZnOAC, 50mM Cacadylate pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.32 | 71.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.511 | α = 90 |
b = 66.511 | β = 90 |
c = 109.192 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | IMAGE PLATE | RIGAKU RAXIS IV | mirrors | 2000-04-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2.1 | 30 | 99.9 | 0.109 | 0.079 | 14.6 | 6.5 | 16917 | 16901 | -3 | 10.5 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.1 | 2.15 | 100 | 0.428 | 0.386 | 3.3 | 14.6 | 1118 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1HZ5 | 2.1 | 24.55 | 16871 | 16869 | 851 | 99.9 | 0.23 | 0.23 | 0.2129 | 0.233 | RANDOM | 21.5 |
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] | |
1.38 | 1.56 | 1.38 | -2.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.9 |
c_scangle_it | 3.53 |
c_scbond_it | 2.46 |
c_mcangle_it | 2.01 |
c_mcbond_it | 1.35 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.63 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1138 |
Nucleic Acid Atoms | |
Solvent Atoms | 136 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
EPMR | phasing |
CNS | refinement |
SCALEPACK | data scaling |