2FUF
Crystal structure of the SV40 large T antigen origin-binding domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TBD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 298 | 1.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.34 | 47.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.669 | α = 90 |
b = 83.669 | β = 90 |
c = 35.88 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | ADSC QUANTUM 315 | crystal | 2005-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 0.9793 | NSLS | X29A |
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 | 1.45 | 50 | 98.7 | 0.07 | 0.07 | 53.6 | 10.9 | 25306 | 24796 | 23.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.45 | 1.5 | 96.3 | 96.3 | 0.441 | 0.441 | 4.5 | 9.7 | 2416 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 1TBD | 1.45 | 50 | 25306 | 24796 | 1252 | 98.74 | 0.17 | 0.17 | 0.169 | 0.189 | RANDOM | 19.648 |
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] | |
-0.2 | -0.1 | -0.2 | 0.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.999 |
r_dihedral_angle_3_deg | 12.112 |
r_dihedral_angle_4_deg | 7.742 |
r_dihedral_angle_1_deg | 6 |
r_scangle_it | 2.671 |
r_scbond_it | 1.791 |
r_mcangle_it | 1.195 |
r_angle_refined_deg | 1.141 |
r_mcbond_it | 0.716 |
r_nbtor_refined | 0.307 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1029 |
Nucleic Acid Atoms | |
Solvent Atoms | 170 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |