2J9N
Robotically harvested Trypsin complexed with Benzamidine containing polypeptide mediated crystal contacts
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1Y5B | PDB ENTRY 1Y5B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 295 | STOCK: 60 MG BOVINE TRYPSIN (SIGMA) PLUS 5 MG BENZAMIDINE (SIGMA) IN 1 ML OF HEPES BUFFER 0.1M PH 7.0 AND 3 MM CACL2. COCKTAIL: 15% PEG 3350 IN 0.1 M HEPES PH 7.0 ALSO CONTAINING 10 MG/ML SALMON SPERM PROTAMINE (SIGMA) DROP: 2 UL STOCK PLUS 2 UL COCKTAIL IN CRYSCHEM PLATES AT 22 DEG C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.924 | α = 90 |
b = 56.695 | β = 90 |
c = 66.054 | 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 | 125 | CCD | Bruker Platinum 135 | MIRROR | 2006-08-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR |
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 | 1.5 | 25.09 | 99.3 | 0.05 | 24.37 | 7.46 | 31641 | 2 |
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 | 1.5 | 1.57 | 95.9 | 0.31 | 3.84 | 3.32 |
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 1Y5B | 1.5 | 25.09 | 31363 | 1664 | 99.8 | 0.155 | 0.154 | 0.176 | RANDOM | 12.45 |
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] | |
-0.1 | 0.08 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.002 |
r_dihedral_angle_4_deg | 15.038 |
r_dihedral_angle_3_deg | 11.833 |
r_dihedral_angle_1_deg | 6.466 |
r_scangle_it | 4.886 |
r_scbond_it | 3.451 |
r_mcangle_it | 2.691 |
r_mcbond_it | 1.739 |
r_angle_refined_deg | 1.324 |
r_angle_other_deg | 0.892 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1708 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
BRUKER | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |
SHAKEANDWARP | phasing |
REFMAC | refinement |