1DUC
EIAV DUTPASE DUDP/STRONTIUM COMPLEX
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1DUP | PDB ENTRY 1DUP |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | DROP: 3.0 MG/ML PROTEIN, 0.05 M IMIDAZOL MALATE BUFFER, PH 7.0, 21% PEG 400, 20 MM SRCL2, 5 MM DUDP; WELL: 0.1 M IMIDAZOLE MALATE BUFFER, PH 7.0, 42% PEG 400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.43 | 64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 106.7 | α = 90 |
b = 106.7 | β = 90 |
c = 106.7 | γ = 90 |
Symmetry | |
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Space Group | P 41 3 2 |
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 | 277 | IMAGE PLATE | MARRESEARCH | MIRRORS | 1995-10-06 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, HAMBURG | BW7B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.05 | 25 | 100 | 0.124 | 0.124 | 17.7 | 10.5 | 13598 | -3 | 22.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.05 | 2.09 | 100 | 0.686 | 0.686 | 3.8 | 10 |
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 | FREE R | PDB ENTRY 1DUP | 2.05 | 20 | 13538 | 668 | 100 | 0.168 | 0.167 | 0.201 | RANDOM | 27.9 |
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] | |
27.9 | 27.9 | 27.9 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_transverse_tor | 26.7 |
p_staggered_tor | 13.4 |
p_scangle_it | 7.8 |
p_scbond_it | 6.1 |
p_planar_tor | 6.1 |
p_mcangle_it | 3.8 |
p_mcbond_it | 2.9 |
p_multtor_nbd | 0.26 |
p_chiral_restr | 0.216 |
p_singtor_nbd | 0.19 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 919 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms | 25 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |