4XVV
Crystal structure of an Acid stress chaperone HdeB (KPN_03484) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277 | 0.2M ammonium sulfate, 30.0% polyethylene glycol monomethyl ether 2000, 0.1M sodium acetate pH 4.6 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.98 | 38.02 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 36.475 | α = 90 |
b = 39.443 | β = 90 |
c = 98.256 | 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 | CCD | ADSC QUANTUM 315 | KOHZU: Double Crystal Si(111) | 2014-10-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.979559 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.7 | 29.286 | 95.4 | 0.052 | 0.069 | 9.32 | 3.62 | 15930 | -3 | 29.463 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.76 | 94.4 | 0.708 | 0.948 | 1.6 |
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 | SAD | THROUGHOUT | 1.7 | 29.286 | 15888 | 808 | 97.77 | 0.198 | 0.1966 | 0.2261 | RANDOM | 33.9187 |
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] | |
-0.42 | 0.49 | -0.07 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.897 |
r_dihedral_angle_4_deg | 24.547 |
r_dihedral_angle_3_deg | 13.73 |
r_dihedral_angle_1_deg | 4.777 |
r_mcangle_it | 2.681 |
r_mcbond_it | 1.711 |
r_mcbond_other | 1.7 |
r_angle_refined_deg | 1.377 |
r_angle_other_deg | 1.124 |
r_chiral_restr | 0.085 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1178 |
Nucleic Acid Atoms | |
Solvent Atoms | 76 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
PDB_EXTRACT | data extraction |
SOLVE | phasing |
XSCALE | data scaling |
REFMAC | refinement |