4RBW
Crystal structure of human alpha-defensin 5, HD5 (Thr7Arg Glu21Arg mutant)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZMP | PDB entry 1ZMP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 294.15 | 0.1M MES pH 6.5, 0.5M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.82 | 32.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 20.55 | α = 90 |
b = 51.703 | β = 96.35 |
c = 50.676 | 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 | PIXEL | PSI PILATUS 6M | 2014-01-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.979 | SSRL | BL12-2 |
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 | 1.5 | 36.08 | 90.5 | 0.089 | 28.6 | 3.1 | 16958 | 15346 |
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 | 1.5 | 1.8 | 93.1 | 0.623 | 2.8 | 3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 1ZMP | 1.5 | 36.077 | 16081 | 14565 | 766 | 90.46 | 0.1841 | 0.18205 | 0.22131 | RANDOM | 25.384 |
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] | |
-0.35 | 0.1 | 1 | -0.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_4_deg | 19.413 |
r_dihedral_angle_3_deg | 13.945 |
r_dihedral_angle_2_deg | 11.691 |
r_dihedral_angle_1_deg | 7.541 |
r_mcangle_it | 3.221 |
r_scbond_it | 3.002 |
r_mcbond_it | 2.197 |
r_mcbond_other | 2.191 |
r_angle_refined_deg | 2.07 |
r_angle_other_deg | 0.871 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1000 |
Nucleic Acid Atoms | |
Solvent Atoms | 75 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |