3DLR
Crystal structure of the catalytic core domain from PFV integrase
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CXU | PDB ENTRY 1cxu |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | 1.0 M ammonium formate, 0.2 M magnesium cloride, 5 mM dithiotreitol, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.79 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 52.14 | ¦Á = 90 |
b = 52.14 | ¦Â = 90 |
c = 239.78 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 2 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2008-01-26 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | CCD | MARMOSAIC 225 mm CCD | 2008-01-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.95373 | ESRF | BM14 |
2 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97837 | ESRF | BM14 |
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 | ||||||||
1,2 | 2.2 | 45.18 | 99.5 | 0.105 | 17.4 | 8.9 | 10584 | 10584 | 32.6 |
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) | |||||||||||
2.2 | 2.32 | 99.3 | 0.681 | 3.4 | 9.3 | 1477 |
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 | SAD | THROUGHOUT | PDB ENTRY 1cxu | 2.2 | 45.18 | 9540 | 1042 | 99.2 | 0.21394 | 0.20905 | 0.25922 | RANDOM | 32.046 |
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] | |
0.82 | 0.41 | 0.82 | -1.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_2_deg | 35.371 |
f_dihedral_angle_4_deg | 16.931 |
f_dihedral_angle_3_deg | 16.041 |
f_dihedral_angle_1_deg | 5.838 |
f_scangle_it | 2.472 |
f_scbond_it | 1.746 |
f_angle_refined_deg | 1.122 |
f_mcangle_it | 1.025 |
f_mcbond_it | 0.558 |
f_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1241 |
Nucleic Acid Atoms | |
Solvent Atoms | 48 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
SHARP | phasing |
REFMAC | refinement |