2Z14
Crystal structure of the N-terminal DUF1126 in human ef-hand domain containing 2 protein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2Z13 | PDB ENTRY 2Z13 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 0.1M Sodium acetate trihydrate, 2.0M Ammonium Sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 38.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.455 | α = 90 |
b = 35.279 | β = 112.64 |
c = 39.15 | 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 | RIGAKU JUPITER 210 | mirrors | 2006-04-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | 1.0 | SPring-8 | BL26B2 |
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 | 1.64 | 50 | 94.2 | 0.033 | 36.1 | 3.54 | 14045 | -3 | 10.4 |
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) | |||||||||||
1.64 | 1.73 | 91.5 | 0.066 | 20.9 |
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 2Z13 | 1.68 | 36.13 | 13058 | 668 | 93.8 | 0.19 | 0.19 | 0.223 | RANDOM | 11.3 |
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] | |
0.4 | 0.25 | 0.13 | -0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.8 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.74 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 983 |
Nucleic Acid Atoms | |
Solvent Atoms | 197 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |