3IB4
The double mutant of Beta-2 microglobulin K58P-W60G
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Z9T | PDB ENTRY 2z9t |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 293 | 0.1M NaAcetate, 0.2M CH3COONH4, 20% Glycerol, 22% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.35 | α = 90 |
b = 28.58 | β = 132.87 |
c = 60.73 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | CCD | ADSC QUANTUM 210 | Sagitally focusing Ge(220) and a multilayer | 2009-02-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9334 | ESRF | ID14-1 |
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 | 1.25 | 19.04 | 99.6 | 0.1 | 15.5 | 10 | 26776 | 8.213 |
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) | |||||||||||
1.25 | 1.32 | 97.2 | 0.692 | 3.2 | 8.7 | 3812 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2z9t | 1.25 | 15 | 25414 | 1355 | 99.56 | 0.15904 | 0.15784 | 0.18118 | RANDOM | 10.92 |
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] | |
-0.05 | -0.04 | 0.04 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.3 |
r_dihedral_angle_4_deg | 18.703 |
r_dihedral_angle_3_deg | 12.255 |
r_dihedral_angle_1_deg | 7.14 |
r_sphericity_free | 3.24 |
r_sphericity_bonded | 2.377 |
r_scangle_it | 2.372 |
r_mcangle_it | 2.194 |
r_scbond_it | 1.694 |
r_mcbond_it | 1.466 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 826 |
Nucleic Acid Atoms | |
Solvent Atoms | 133 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
MOLREP | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |