4QR9
Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1CKT | PDB entry 1CKT |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 277 | 0.025M Sodium Cacodylate 0.020M Magnesium Chloride 2.5% MPD (equilibrated against 40% MPD), pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.82 | 56.37 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 42.751 | α = 90 |
b = 84.17 | β = 90 |
c = 94.227 | 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 | PSI PILATUS 6M | Mirrors | 2013-07-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.97949 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 42.12 | 98.9 | 0.113 | 16.025 | 7.1 | 23702 | 23441 | -3 | 32 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.07 | 93.5 | 0.658 | 1.9 | 5.1 | 2162 |
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 | PDB entry 1CKT | 2 | 42.12 | 22219 | 1176 | 98.78 | 0.19868 | 0.19675 | 0.23387 | RANDOM | 42.412 |
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] | |
2.43 | -1.21 | -1.22 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.956 |
r_dihedral_angle_4_deg | 18.229 |
r_dihedral_angle_3_deg | 18.187 |
r_dihedral_angle_1_deg | 5.485 |
r_angle_other_deg | 2.924 |
r_angle_refined_deg | 1.622 |
r_chiral_restr | 0.098 |
r_bond_refined_d | 0.016 |
r_bond_other_d | 0.012 |
r_gen_planes_refined | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1234 |
Nucleic Acid Atoms | 808 |
Solvent Atoms | 115 |
Heterogen Atoms | 1 |
Software
Software | |
---|---|
Software Name | Purpose |
Xaloc | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |