3I38
Structure of a putative chaperone protein dnaj from klebsiella pneumoniae subsp. pneumoniae mgh 78578
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 294 | 0.2M Ammonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.48 | 50.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.805 | α = 81.75 |
b = 61.626 | β = 78.71 |
c = 92.907 | γ = 83.79 |
Symmetry | |
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Space Group | P 1 |
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 | MIRROR | 2009-06-18 | M | SAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | APS | 21-ID-F |
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 | 2.2 | 90.54 | 98 | 0.07 | 0.07 | 30.081 | 3.9 | 66358 | -3 |
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 | 2.2 | 2.24 | 97.6 | 0.559 | 0.559 | 2 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 2.3 | 90.54 | 57758 | 57758 | 2941 | 98.09 | 0.219 | 0.217 | 0.262 | RANDOM | 25.41 |
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] | |
0.83 | -1.77 | 1.29 | -1.03 | 0.8 | -0.16 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.539 |
r_dihedral_angle_4_deg | 12.921 |
r_dihedral_angle_3_deg | 10.584 |
r_scangle_it | 4.123 |
r_scbond_it | 2.594 |
r_dihedral_angle_1_deg | 2.524 |
r_mcangle_it | 1.746 |
r_angle_refined_deg | 1.743 |
r_mcbond_it | 0.986 |
r_angle_other_deg | 0.893 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9275 |
Nucleic Acid Atoms | |
Solvent Atoms | 186 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
HKL-3000 | phasing |
MLPHARE | phasing |
DM | model building |
SHELXD | phasing |
RESOLVE | model building |
CCP4 | model building |
ARP/wARP | model building |
Coot | model building |
REFMAC | refinement |
ADSC | data collection |
HKL-2000 | data scaling |
DM | phasing |
RESOLVE | phasing |
ARP | model building |
CCP4 | phasing |