2DQK
Crystal structure of the complex of proteinase K with a specific lactoferrin peptide Val-Leu-Leu-His at 1.93 A resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3PRK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | sodium nitrate, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 42.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.313 | α = 90 |
b = 68.313 | β = 90 |
c = 108.407 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | 291 | IMAGE PLATE | MAR scanner 345 mm plate | mirror | 2006-05-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.93 | 57.74 | 98.6 | 19884 | 19884 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.93 | 1.96 | 99.2 |
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 | 3PRK | 1.93 | 57.74 | 19884 | 18805 | 1012 | 99.19 | 0.16 | 0.1536 | 0.15182 | 0.1871 | RANDOM | 13.263 |
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 | -0.16 | 0.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 15.529 |
r_dihedral_angle_1_deg | 3.848 |
r_scangle_it | 3.315 |
r_scbond_it | 1.931 |
r_angle_refined_deg | 1.318 |
r_mcangle_it | 0.996 |
r_mcbond_it | 0.496 |
r_symmetry_vdw_refined | 0.232 |
r_nbd_refined | 0.213 |
r_symmetry_hbond_refined | 0.161 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2064 |
Nucleic Acid Atoms | |
Solvent Atoms | 291 |
Heterogen Atoms | 5 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
SCALEPACK | data scaling |
AMoRE | phasing |