5MAJ
CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morpholino-1,3,5-triazine-2-carbonitrile
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 295 | 25% PEG3350, 0.2M ammonium acetate, 0.1M HEPES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 45.7 | α = 90 |
b = 57.061 | β = 90 |
c = 75.266 | 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 | PIXEL | DECTRIS PILATUS 6M | 2015-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0000 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 45.51 | 96.1 | 0.0342 | 13.8 | 6.06 | 102712 |
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 | 1 | 1.09 | 90.3 | 0.5485 | 2 | 5.43 | 24065 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1 | 45.51 | 97604 | 5040 | 96.12 | 0.13806 | 0.13639 | 0.16999 | RANDOM | 17.517 |
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] | |
0.21 | -0.65 | 0.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.57 |
r_sphericity_free | 25.026 |
r_dihedral_angle_4_deg | 15.497 |
r_sphericity_bonded | 13.88 |
r_dihedral_angle_3_deg | 13.129 |
r_rigid_bond_restr | 7.932 |
r_dihedral_angle_1_deg | 5.898 |
r_long_range_B_refined | 4.257 |
r_scbond_it | 3.465 |
r_mcangle_it | 2.809 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1688 |
Nucleic Acid Atoms | |
Solvent Atoms | 399 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XPREP | data reduction |
XSCALE | data scaling |
PHASER | phasing |