8PQM
The DNA-binding domain of L-lactate utilization repressor (LutR-DBD) from Bacillus subtilis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291 | Morpheus screen solution: 0.1 M sodium HEPES/MOPS (acid) buffer system (pH 7.5), 37.5% (v/v) 2 methyl 2,4 pentanediol, 37.5% (v/v) PEG 1000, 37.5% (v/v) PEG 3350, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI Volume ratio (protein:solution) = 1ul : 2ul Plate: EasyXtal 15 well plate (NeXtal Biotechnologies, Holland) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.79 | 30.83 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 28.31 | α = 90 |
b = 38.37 | β = 90 |
c = 66.71 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | 2022-09-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9797 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.46 | 50 | 100 | 0.067 | 0.073 | 0.9990000000000001 | 12.26 | 6.76 | 24387 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.46 | 1.55 | 3.1189999999999998 | 3.388 | 0.319 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.46 | 33.38 | 12527 | 660 | 99.98 | 0.20402 | 0.20221 | 0.2086 | 0.23735 | 0.239 | RANDOM | 40.221 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.77 | -0.95 | 0.18 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 14.925 |
r_dihedral_angle_2_deg | 13.993 |
r_long_range_B_refined | 13.299 |
r_long_range_B_other | 13.038 |
r_scangle_other | 7.679 |
r_mcangle_it | 7.112 |
r_mcangle_other | 7.111 |
r_dihedral_angle_1_deg | 6.272 |
r_scbond_other | 5.15 |
r_scbond_it | 5.147 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 593 |
Nucleic Acid Atoms | |
Solvent Atoms | 72 |
Heterogen Atoms | 2 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
XDS | data reduction |
MOLREP | phasing |