2Q10
RESTRICTION ENDONUCLEASE BcnI (WILD TYPE)-COGNATE DNA SUBSTRATE COMPLEX
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 294 | 0.02 M CALCIUM CHLORIDE DIHYDRATE, 0.1 M SODIUM ACETATE TRIHYDRATE, 30% (V/V) 2-METHYL-2,4-PENTANEDIOL , pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.05 | 40.07 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 81.354 | α = 90 |
b = 87.551 | β = 90 |
c = 79.162 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 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 | 2006-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MPG/DESY, HAMBURG BEAMLINE BW6 | MPG/DESY, HAMBURG | BW6 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.75 | 30 | 99.9 | 0.079 | 5.8 | 3.2 | 57635 | 57635 | 14.8 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.75 | 1.84 | 100 | 0.26 | 2.9 | 3.2 | 8336 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2ODI | 1.75 | 29.72 | 57579 | 57579 | 2882 | 99.8 | 0.176 | 0.176 | 0.174 | 0.213 | RANDOM | 8.32 |
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 | 0.68 | -0.88 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.949 |
r_dihedral_angle_4_deg | 18.347 |
r_dihedral_angle_3_deg | 12.796 |
r_dihedral_angle_1_deg | 6.688 |
r_scangle_it | 2.237 |
r_scbond_it | 1.8 |
r_angle_refined_deg | 1.35 |
r_mcangle_it | 1.032 |
r_angle_other_deg | 0.911 |
r_mcbond_it | 0.799 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3844 |
Nucleic Acid Atoms | 890 |
Solvent Atoms | 645 |
Heterogen Atoms | 5 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MAR345 | data collection |
MOSFLM | data reduction |
SCALA | data scaling |