6S48
AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6G3B |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Morpheus screen H1 conditions: 0.02 M of L-Na-glutamate, alanine (racemic), glycine, lysine HCl (racemic), serine (racemic), 0.1 M buffer (1 M Imidazole, 1 M MES, pH 6.5), 30% precipitant (20% w/v PEG 20 000, 40% v/v PEG MME 550) |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 37.129 | α = 90 |
b = 116.21 | β = 102.91 |
c = 56.774 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2019-05-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.918400 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.9 | 40.07 | 98.5 | 0.081 | 0.094 | 0.998 | 10.55 | 3.8 | 36585 | 36.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.9 | 2.01 | 97.6 | 0.807 | 0.943 | 0.615 | 1.43 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 6G3B | 1.9 | 40.07 | 34760 | 1825 | 98.59 | 0.17826 | 0.17621 | 0.21671 | RANDOM | 35.854 |
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] | |
-0.72 | -0.35 | -1.27 | 1.95 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.952 |
r_dihedral_angle_4_deg | 16.556 |
r_dihedral_angle_3_deg | 15.314 |
r_long_range_B_refined | 5.562 |
r_long_range_B_other | 5.368 |
r_dihedral_angle_1_deg | 5.159 |
r_scangle_other | 3.118 |
r_mcangle_other | 2.856 |
r_mcangle_it | 2.855 |
r_scbond_it | 1.874 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3720 |
Nucleic Acid Atoms | 893 |
Solvent Atoms | 487 |
Heterogen Atoms | 46 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
BALBES | phasing |
ARP/wARP | model building |
Coot | model building |