4WQ2
Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4PHJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 294 | 3 UL PROTEIN (10 MG/ML PEF(S), 5 MM SODIUM CACODYLATE, 2 MM EDTA, 5 MM BME, 1 MM CALCIUM CHLORIDE, PH 7.0) + 3 UL PRECIPITANT (50 MM SODIUM CACODYLATE, 12.5% PEG6000, 20 MM CALCIUM CHLORIDE, PH 7.0) + 1 UL WATER |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.72 | α = 90 |
b = 78.43 | β = 91.12 |
c = 56.3 | 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 | PIXEL | DECTRIS PILATUS 6M | 2013-03-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.64 | 41.99 | 97.5 | 0.052 | 0.031 | 0.997 | 16.1 | 3.7 | 51550 | 51550 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.64 | 1.68 | 96.5 | 0.901 | 0.547 | 0.666 | 1.7 | 3.6 | 3749 |
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 | 4phj | 1.64 | 41.99 | 48906 | 2620 | 97.33 | 0.1713 | 0.1699 | 0.1966 | RANDOM | 34.082 |
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] | |
-0.14 | -0.38 | 1.07 | -0.91 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.424 |
r_dihedral_angle_4_deg | 21.246 |
r_dihedral_angle_3_deg | 15.979 |
r_dihedral_angle_1_deg | 5.192 |
r_mcangle_it | 3.058 |
r_mcbond_it | 2.203 |
r_mcbond_other | 2.203 |
r_angle_refined_deg | 1.967 |
r_angle_other_deg | 1.004 |
r_chiral_restr | 0.142 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2806 |
Nucleic Acid Atoms | |
Solvent Atoms | 157 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
xia2 | data reduction |
PHASER | phasing |