4UZC
KSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP SETUP AT 20 DEGREE CENTIGRADE. AFTER TWO DAYS, CRYSTALS WERE DETACHED FROM THE CARRIER PLASTIC BY ADDING 1 UL OF 2 M AMMONIUM FORMATE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.79 | 55.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 103.18 | α = 90 |
b = 103.18 | β = 90 |
c = 228.25 | γ = 120 |
Symmetry | |
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Space Group | P 65 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 | PIXEL | DECTRIS PILATUS 6M | MIRRORS | 2014-03-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 |
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 | 3.7 | 89.36 | 95.9 | 0.23 | 18.53 | 29.7 | 7874 | 2 | 119.8 |
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 | 3.7 | 3.84 | 99.1 | 1.92 | 31.3 |
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 | PDB ENTRY 2YPY | 3.7 | 89.36 | 7485 | 389 | 95.83 | 0.20278 | 0.20078 | 0.2386 | RANDOM | 115.815 |
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] | |
-2 | -1 | -2 | 6.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.5 |
r_dihedral_angle_3_deg | 14.491 |
r_dihedral_angle_4_deg | 12.955 |
r_mcangle_it | 12.583 |
r_mcbond_it | 7.888 |
r_mcbond_other | 7.885 |
r_scbond_it | 7.588 |
r_dihedral_angle_1_deg | 3.332 |
r_angle_refined_deg | 0.508 |
r_angle_other_deg | 0.492 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4316 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |