2NLP
Human beta-defensin-1 (Mutant Gln24Glu)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 293 | LITHIUM SULFATE, HEPES, pH 7.5, vapor diffusion, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.68 | α = 90 |
b = 27.68 | β = 113.6 |
c = 58.23 | 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 | IMAGE PLATE | MAR scanner 345 mm plate | Osmic mirrors | 2005-12-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.54178 |
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 | 1.85 | 40 | 96.4 | 0.058 | 27 | 6.2 | 12081 | 12081 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1.85 | 1.92 | 94 | 0.304 | 6.1 | 6.1 | 1143 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1IJV | 1.85 | 30 | 12078 | 12078 | 582 | 96.32 | 0.179 | 0.179 | 0.176 | 0.237 | RANDOM | 23.923 |
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] | |
-1.49 | -1.07 | 1.19 | -0.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.603 |
r_dihedral_angle_4_deg | 23.071 |
r_dihedral_angle_3_deg | 13.861 |
r_dihedral_angle_1_deg | 6.237 |
r_scangle_it | 4.059 |
r_scbond_it | 2.837 |
r_mcangle_it | 1.781 |
r_angle_refined_deg | 1.698 |
r_mcbond_it | 1.12 |
r_nbtor_refined | 0.306 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1084 |
Nucleic Acid Atoms | |
Solvent Atoms | 278 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |