5THK
Crystal Structure of a Putative Dehydrogenase from Burkholderia cenocepacia with bound NADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | BuceA.00010.k.B1.PW37237 @22.1 mg/ml, incubated with 4mM NADP, mixed 1:1 with an equal volume MCSG1(e3): 30% (v/v) PEG 550 MME, 0.1 M HEPES/NaOH, pH=7.5, 0.05 M MgCl2 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.07 | 40.64 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 75.54 | α = 90 |
b = 102.44 | β = 97.28 |
c = 122.25 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 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 | MARMOSAIC 300 mm CCD | Beryllium Lenses | 2016-07-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.4 | 99.1 | 0.062 | 0.999 | 14.28 | 3.8 | 358521 | -3 | 10.35 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.4 | 1.44 | 98.7 | 0.56 | 0.769 | 2.38 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3U5T | 1.4 | 45.192 | 1.34 | 358467 | 1987 | 99.09 | 0.1399 | 0.1397 | 0.1641 | 14.7035 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.915 |
f_angle_d | 0.846 |
f_chiral_restr | 0.084 |
f_plane_restr | 0.006 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 15355 |
Nucleic Acid Atoms | |
Solvent Atoms | 2823 |
Heterogen Atoms | 434 |
Software
Software | |
---|---|
Software Name | Purpose |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |