4E88
CRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3U13 | pdb entry 3U13 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277 | Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M REMARK 280 NH4F, 20% PEG3350, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M , VAPOR DIFFUSION, SITTING DROP, temperature 277KK |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.994 | α = 90 |
b = 61.745 | β = 128.95 |
c = 59.384 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2011-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 30 | 97.3 | 0.046 | 30.9 | 3.8 | 16356 | -3 | 28.24 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MIR | THROUGHOUT | pdb entry 3U13 | 2 | 23.091 | 1.38 | 16344 | 828 | 97.27 | 0.18 | 0.178 | 0.215 | random | 33.286 |
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] | |
0.61 | 1.933 | 6.468 | -7.078 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.511 |
f_angle_d | 1.073 |
f_chiral_restr | 0.077 |
f_bond_d | 0.007 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1586 |
Nucleic Acid Atoms | |
Solvent Atoms | 183 |
Heterogen Atoms | 6 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
BALBES | phasing |