3DUY
Crystal structure of human beta-secretase in complex with NVP-AFJ144
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FKN | PDB entry 1FKN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 1.0M Ammonium sulfate in water, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K. Protein stock was BACE MUT46B batch XII 8.5 mg/mL in 10mM Tris-HCl pH 7.4, 25mM NaCl, with a 5-fold excess of NVP-AFJ144-NX-2 added from a 50mM stock solution in 90% DMSO-D6 (1.8% DMSO in drop). A solution containing 1.2M Ammonium sulfate, 25% Glycerol, 1mM NVP-AFJ144-NX-2 and 1.8% DMSO was used as cryo-protectant |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.537 | α = 90 |
b = 103.062 | β = 103.64 |
c = 100.602 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | RIGAKU SATURN 92 | Mirrors | 2005-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 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 | 1.97 | 70.93 | 93.5 | 0.068 | 22.55 | 10.2 | 107931 | 107931 | -3 | 33.092 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.97 | 2.03 | 61.7 | 0.395 | 3.8 | 4.7 | 6065 |
Refinement
Statistics | |||||||||||||||||||
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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 1FKN | 1.97 | 70.93 | 107931 | 107931 | 10413 | 93.4 | 0.204 | 0.204 | 0.202 | 0.223 | RANDOM | 35.063 |
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] | |
-1.27 | -0.09 | 2.16 | -0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.5 |
c_scangle_it | 3.02 |
c_mcangle_it | 2.34 |
c_scbond_it | 2 |
c_mcbond_it | 1.47 |
c_angle_deg | 0.8 |
c_improper_angle_d | 0.62 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8777 |
Nucleic Acid Atoms | |
Solvent Atoms | 750 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
CNX | phasing |
CNX | refinement |