1AP2
SINGLE CHAIN FV OF C219
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IGM | PDB ENTRY 1IGM |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.5 | THE PROTEIN WAS CRYSTALLIZED IN 21% PEG 6000, 100 MM SODIUM CITRATE PH 4.5, IN HANGING DROPS CONTAINING SUBTILISIN CARLSBERG IN A 1:100 MOLAR RATIO., vapor diffusion - hanging drop THE DEPOSITORS CRYSTALLIZED THE SINGLE CHAIN FV IN THE PRESENCE OF SUBTILISIN, AS DESCRIBED IN THE PRIMARY REFERENCE. THE SEQUENCE OF THE SINGLE CHAIN IS DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLNSGNQKNYLTWYQQKPGQPPKLLIYWAS TRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDYSYPLTFGAGTKLEP (LIGHT CHAINS A AND C) GGGGSGGGGSGKSGGGG (LINKER) EVQLQQSGAELVRPGASVKLSCTASGFNIKDDFMHWVKQRPEQGLEWIGRIDPANDNT KYAPKFQDKATIIADTSSNTAYLQLSSLTSEDTAVYYCARREVYSYYSPLDVWGAGTT VTVPSG (HEAVY CHAINS B AND D) SEQKLISEEDLNHHHHH (C-MYC TAG + 5XHIS TAG) THE DEPOSITORS HAVE NOT DETERMINED WHERE SUBTILISIN CLEAVES EXACTLY, BUT THE MOBILITY ON SDS GELS SUGGESTS THAT THE MOST OF THE LINKER AND MOST OF BOTH TAGS ARE REMOVED. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.85 | 58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.04 | α = 90 |
b = 64.35 | β = 90 |
c = 154.11 | 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 | 298 | AREA DETECTOR | XUONG-HAMLIN MULTIWIRE | 1997-05-13 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
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 | 2.36 | 50 | 91.6 | 0.098 | 9.7 | 3.6 | 22616 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.36 | 2.55 | 76.1 | 0.277 | 2.8 | 2.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 1IGM | 2.36 | 6 | 2 | 19352 | 1519 | 78.4 | 0.2045 | 0.2045 | 0.284 | RANDOM | 10.77 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 30.29 |
x_mcangle_it | 8.01 |
x_mcbond_it | 6.343 |
x_scbond_it | 2.957 |
x_scangle_it | 2.931 |
x_angle_deg | 1.121 |
x_improper_angle_d | 0.572 |
x_bond_d | 0.006 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3620 |
Nucleic Acid Atoms | |
Solvent Atoms | 102 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SDMS | data collection |
SDMS | data reduction |
X-PLOR | model building |
X-PLOR | refinement |
SDMS | data scaling |
X-PLOR | phasing |