3QNW
Caspase-6 in complex with Z-VAD-FMK inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.3 | 298 | 0.1 M lithium sulfate, 0.1 M sodium citrate, 11% 2-propanol , VAPOR DIFFUSION, temperature 298K, pH 4.3 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.206 | α = 90 |
b = 65.446 | β = 91.24 |
c = 91.718 | 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 | ADSC QUANTUM 315 | 2010-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9763 | Diamond | I04 |
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 | 2.65 | 29.1 | 99.2 | 0.114 | 14.8 | 7.5 | 30244 | 30002 |
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 | 2.65 | 2.79 | 98.8 | 0.564 | 3.6 | 7.6 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2wdp | 2.65 | 29.1 | 28824 | 28380 | 1505 | 98.46 | 0.24275 | 0.24038 | 0.28713 | RANDOM | 24.792 |
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] | |
1.31 | -0.02 | -2.25 | 0.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.767 |
r_dihedral_angle_4_deg | 17.694 |
r_dihedral_angle_3_deg | 13.3 |
r_dihedral_angle_1_deg | 5.004 |
r_scangle_it | 0.857 |
r_angle_refined_deg | 0.815 |
r_angle_other_deg | 0.746 |
r_mcangle_it | 0.657 |
r_scbond_it | 0.528 |
r_mcbond_it | 0.353 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6898 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
GDA | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |