6BI7
Crystal structure of Rev7-WT/Rev3 as a monomer under high-salt conditions
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6BC8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289.15 | hRev7/3 at 60 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4 was mixed in a 1:1 ratio with a well solution consisting of 100 mM sodium citrate, 1M LiCl, 7.5% (w/v) PEG6000 at pH=4.75. Crystals were frozen in the reservoir solution with the addition of 20% (w/v) sucrose |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.696 | α = 90 |
b = 89.696 | β = 90 |
c = 284.841 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 77 | PIXEL | DECTRIS PILATUS3 S 6M | 2016-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CHESS BEAMLINE F1 | 0.976 | CHESS | F1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | 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 | 2.8 | 284.84 | 99.8 | 0.044 | 21.1 | 9.6 | 33727 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.8 | 2.85 | 99.9 | 0.168 | 0.946 | 2.2 | 9.5 |
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 | 6BC8 | 2.8 | 284.84 | 33727 | 1715 | 99.75 | 0.2778 | 0.2754 | 0.3213 | RANDOM | 94.6819 |
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] | |
-3.5 | -1.75 | -3.5 | 11.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.701 |
r_dihedral_angle_4_deg | 22.302 |
r_dihedral_angle_3_deg | 17.212 |
r_mcangle_it | 11.895 |
r_mcbond_it | 7.657 |
r_mcbond_other | 7.656 |
r_dihedral_angle_1_deg | 7.617 |
r_angle_other_deg | 3.518 |
r_angle_refined_deg | 1.527 |
r_chiral_restr | 0.088 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6426 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data processing |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
Coot | model building |