3IQL
Crystal structure of the rat endophilin-A1 SH3 domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1GCQ | PDB entry 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 277 | 20% methyl-2,4-pentanediol, 0.1M sodium acetate, 0.05M calcium chloride, 10mM 2-mercaptoethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.338 | α = 90 |
b = 34.156 | β = 107.79 |
c = 62.729 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 4 | 2007-11-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE A1 | 0.97720 | CHESS | A1 |
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 | 1.4 | 30 | 96.3 | 0.031 | 30.2 | 3 | 24510 | 23667 | 2 | 8.5 |
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) | |||||||||||
1.4 | 1.5 | 85.5 | 0.071 | 11.1 | 1.9 | 4701 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW | 1.4 | 30 | 24901 | 23667 | 1234 | 96.56 | 0.12837 | 0.12702 | 0.15358 | RANDOM | 13.739 |
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] | |
1 | 0.14 | -0.27 | -0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.769 |
r_dihedral_angle_4_deg | 22.324 |
r_dihedral_angle_3_deg | 13.004 |
r_dihedral_angle_1_deg | 6.311 |
r_sphericity_free | 6.116 |
r_scangle_it | 3.908 |
r_sphericity_bonded | 3.734 |
r_scbond_it | 3.697 |
r_rigid_bond_restr | 3.433 |
r_mcangle_it | 2.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1174 |
Nucleic Acid Atoms | |
Solvent Atoms | 192 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |