5Y1K
Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2-chlorobenzyl)ureido)-N-hydroxy-4-methylpentanamide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 0.1M Tris, pH 8.5, 0.2M Magnesium chloride, 24% PEG 2000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.275 | α = 90 |
b = 109.254 | β = 90 |
c = 111.884 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RIGAKU RAXIS IV | 2016-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.81 | 23.71 | 99.9 | 0.05 | 0.055 | 0.022 | 0.998 | 25.6 | 6 | 83333 | 25.28 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.81 | 1.87 | 100 | 0.21 | 0.231 | 0.095 | 0.984 | 8.11 | 5.8 |
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 | 4X2U | 1.81 | 23.71 | 78262 | 4002 | 98.43 | 0.1716 | 0.1695 | 0.213 | RANDOM | 27.482 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.56 |
r_dihedral_angle_4_deg | 18.168 |
r_dihedral_angle_3_deg | 13.438 |
r_dihedral_angle_1_deg | 6.391 |
r_angle_refined_deg | 1.881 |
r_angle_other_deg | 1.078 |
r_chiral_restr | 0.122 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7308 |
Nucleic Acid Atoms | |
Solvent Atoms | 461 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
DENZO | data collection |
SCALEPACK | data scaling |
MOLREP | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |