4OU3
Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4FKE | PDB ENTRY 4FKE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 277 | 2 uL protein + 2 uL well solution (18% v/v PEG3350, 200 mM lithium sulfate, 100 mM HEPES, pH 7.2), VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.17 | 61.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 260.323 | α = 90 |
b = 62.879 | β = 100.59 |
c = 82.023 | 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 | CCD | NOIR-1 | 2013-01-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | ALS | 4.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.92 | 50 | 97.9 | 0.079 | 0.079 | 20.7 | 3.8 | 95642 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.92 | 1.96 | 97 | 0.615 | 0.615 | 1.7 | 3.9 |
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 | PDB ENTRY 4FKE | 1.95 | 50 | 88648 | 4699 | 97.85 | 0.14285 | 0.14038 | 0.18956 | RANDOM | 49.799 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.59 | -0.35 | 0.35 | 0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_bonded | 43.043 |
r_dihedral_angle_2_deg | 40.055 |
r_sphericity_free | 22.47 |
r_dihedral_angle_4_deg | 16.523 |
r_dihedral_angle_3_deg | 14.424 |
r_long_range_B_refined | 10.931 |
r_scbond_it | 10.842 |
r_mcangle_it | 6.611 |
r_dihedral_angle_1_deg | 6.328 |
r_mcbond_it | 5.551 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7281 |
Nucleic Acid Atoms | |
Solvent Atoms | 906 |
Heterogen Atoms | 303 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CCP4 | phasing |