6QM2
NlaIV restriction endonuclease
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 294 | 10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'-CAGGTACCATG-3' strands. The protein-DNA solutions were in turn mixed in 1:1 ratio with the precipitant solution containing 2 M NaCl and 100 mM citric acid, pH 5. |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 110.38 | α = 90 |
b = 110.38 | β = 90 |
c = 209.006 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 62 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | BENT MIRROR | 2008-12-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | 1.05 | MPG/DESY, HAMBURG | BW6 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.8 | 30 | 98.5 | 0.043 | 0.04 | 28.92 | 7.5 | 18997 |
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 | 2.8 | 2.97 | 98.6 | 1.052 | 0.986 | 1.72 | 7.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.8 | 29.72 | 18083 | 912 | 98.46 | 0.19245 | 0.19095 | 0.22103 | RANDOM | 115.889 |
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] | |
1.68 | 0.84 | 1.68 | -5.44 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.834 |
r_dihedral_angle_4_deg | 16.289 |
r_dihedral_angle_3_deg | 13.639 |
r_long_range_B_refined | 9.963 |
r_long_range_B_other | 9.927 |
r_scangle_other | 6.542 |
r_mcangle_it | 6.427 |
r_mcangle_other | 6.427 |
r_dihedral_angle_1_deg | 5.289 |
r_mcbond_it | 3.825 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2056 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
STARANISO | data scaling |
autoSHARP | phasing |
SHELXDE | phasing |
SOLOMON | phasing |
DM | phasing |
PARROT | phasing |
ARP/wARP | model building |
BUCCANEER | model building |