3A8K
Crystal Structure of ETD97N-EHred complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3A8J |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 288 | 14.4% PEG8000, 0.036M KH2PO4, 18% Glycerol, 0.05M NaCl, 1mM CTAB, 1mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.122 | α = 91.56 |
b = 88.412 | β = 102.42 |
c = 97.863 | γ = 89.59 |
Symmetry | |
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Space Group | P 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 | Bruker DIP-6040 | 2008-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9000 | SPring-8 | BL44XU |
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 | 1.95 | 50 | 98.3 | 0.071 | 20.9 | 4 | 119927 |
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 | 1.95 | 1.98 | 0.442 | 3.2 | 3.9 |
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 | 3A8J | 1.95 | 43.97 | 119927 | 6363 | 98.09 | 0.1739 | 0.17094 | 0.22915 | RANDOM | 25.512 |
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] | |
0.05 | 0.21 | -0.87 | -0.52 | -0.06 | 0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.079 |
r_dihedral_angle_4_deg | 17.138 |
r_dihedral_angle_3_deg | 15.331 |
r_dihedral_angle_1_deg | 6.608 |
r_scangle_it | 5.017 |
r_scbond_it | 3.221 |
r_mcangle_it | 1.971 |
r_angle_refined_deg | 1.867 |
r_mcbond_it | 1.192 |
r_chiral_restr | 0.141 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13164 |
Nucleic Acid Atoms | |
Solvent Atoms | 1495 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |