3PBX
Strontium bound to the sequence d(CCGGCGCCGG)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GOJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 290 | SrCl2, MPD, NaCacodylate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.89 | α = 90 |
b = 25.001 | β = 110.01 |
c = 37.044 | 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 | OXFORD SAPPHIRE CCD | multi-graded optics | 2007-02-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 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 | 1.879 | 14.866 | 78.55 | 0.045 | 2.1 | 4705 | 3706 | 1 | 1 | 27.446 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.879 | 1.927 |
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 | 3GOJ | 1.879 | 14.86 | 3531 | 175 | 78.55 | 0.2544 | 0.2508 | 0.32701 | RANDOM | 27.446 |
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] | |
-3.38 | 0.31 | 3.36 | 0.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 4.016 |
r_angle_refined_deg | 3.666 |
r_scbond_it | 3.007 |
r_symmetry_hbond_refined | 0.434 |
r_xyhbond_nbd_refined | 0.389 |
r_nbtor_refined | 0.344 |
r_nbd_refined | 0.259 |
r_metal_ion_refined | 0.172 |
r_chiral_restr | 0.15 |
r_symmetry_vdw_refined | 0.106 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 404 |
Solvent Atoms | 57 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
CrysalisPro | data collection |
MOLREP | phasing |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |