2NLF
Human beta-defensin-1 (Mutant Leu13Glu)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IJV | PDB entry 1IJV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.6 | 293 | PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, vapor diffusion, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 51.04 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.01 | α = 90 |
b = 46.79 | β = 97.3 |
c = 28.56 | 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 | 2004-12-10 | 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 | 1.45 | 40 | 99 | 0.07 | 18 | 4.5 | 13851 | 13851 | -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) | |||||||||||
1.45 | 1.5 | 97.2 | 0.189 | 5.8 | 3.6 | 1365 |
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 | 1.45 | 30 | 13844 | 13844 | 988 | 98.96 | 0.143 | 0.143 | 0.14 | 0.184 | RANDOM | 13.457 |
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] | |
0.16 | 0.01 | -0.11 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 43.743 |
r_dihedral_angle_4_deg | 32.131 |
r_dihedral_angle_3_deg | 10.307 |
r_dihedral_angle_1_deg | 6.25 |
r_scangle_it | 4.424 |
r_scbond_it | 3.427 |
r_mcangle_it | 2.512 |
RIGID-BOND RESTRAINTS (A**2) | 1.987 |
r_mcbond_it | 1.871 |
r_angle_refined_deg | 1.672 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 574 |
Nucleic Acid Atoms | |
Solvent Atoms | 230 |
Heterogen Atoms | 20 |
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 |