3M6K
Crystal Structure of N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 303 | 0.1 M phosphate-citrate pH 5, 0.2 M NaCl, 16% PEG 8000, 1M Guanidium hydrochloride, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.09 | α = 90 |
b = 70.09 | β = 90 |
c = 349.63 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | 78 | CCD | RAYONIX MX-225 | beryllium lenses | 2008-04-23 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 78 | CCD | RAYONIX MX-225 | 2008-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97872 | APS | 21-ID-G |
2 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.97915 | APS | 21-ID-D |
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 | 2.6 | 29.5 | 99.9 | 0.079 | 0.074 | 19 | 8.1 | 28160 | 28151 | 42.1 |
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) | ||||||||||
2.6 | 2.72 | 100 | 0.572 | 0.522 | 3.2 | 6 | 3331 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.6 | 29.14 | 28151 | 26710 | 1438 | 99.96 | 0.24371 | 0.24371 | 0.24132 | 0.28883 | RANDOM | 55.918 |
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] | |
2.02 | 2.02 | -4.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.326 |
r_dihedral_angle_4_deg | 18.828 |
r_dihedral_angle_3_deg | 17.444 |
r_dihedral_angle_1_deg | 5.538 |
r_scangle_it | 1.464 |
r_angle_refined_deg | 1.203 |
r_scbond_it | 0.968 |
r_angle_other_deg | 0.89 |
r_mcangle_it | 0.58 |
r_mcbond_it | 0.522 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5967 |
Nucleic Acid Atoms | |
Solvent Atoms | 30 |
Heterogen Atoms | 15 |
Software
Software | |
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Software Name | Purpose |
MD2-microdiffractometer | data collection |
SHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |