3F67
Crystal Structure of Putative Dienelactone Hydrolase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 289 | 0.2M Li2SO4 0.1 M Tris pH 7.0 1.0 M K/Na tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.82 | 56.46 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 106.385 | α = 90 |
b = 106.385 | β = 90 |
c = 53.581 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 41 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 | SBC-3 | mirrors | 2008-10-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9792 | APS | 19-BM |
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 | 1.74 | 47.85 | 99.8 | 0.109 | 7.6 | 14 | 31820 | 31820 | 24.19 |
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 | 1.74 | 1.78 | 100 | 0.866 | 2.4 | 10.3 | 1583 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.74 | 47.85 | 29596 | 29596 | 1565 | 97.94 | 0.169 | 0.169 | 0.168 | 0.198 | RANDOM | 19.911 |
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] | |
-0.23 | -0.23 | 0.45 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.012 |
r_dihedral_angle_3_deg | 14.858 |
r_dihedral_angle_4_deg | 12.501 |
r_dihedral_angle_1_deg | 6.19 |
r_scangle_it | 3.719 |
r_scbond_it | 2.367 |
r_angle_refined_deg | 1.547 |
r_mcangle_it | 1.503 |
r_mcbond_it | 0.877 |
r_chiral_restr | 0.136 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1881 |
Nucleic Acid Atoms | |
Solvent Atoms | 295 |
Heterogen Atoms | 14 |
Software
Software | |
---|---|
Software Name | Purpose |
SBC-Collect | data collection |
HKL-3000 | data collection |
HKL-3000 | phasing |
MLPHARE | phasing |
DM | model building |
SHELXD | phasing |
RESOLVE | model building |
Coot | model building |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
DM | phasing |
RESOLVE | phasing |