3RCB
Crystal structure of the K102E mutant of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex with TDP-benzene and NADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3RBV | model generated using binary complex, PDB entry 3RBV |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 298 | 1.2 M sodium/potassium phosphate, 100 mM HEPPS, 5 mM TDP-benzene, 5 mM NADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.46 | 64.47 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 72.371 | α = 90 |
b = 103.497 | β = 90 |
c = 145.154 | γ = 90 |
Symmetry | |
---|---|
Space Group | I 2 2 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 | Bruker Platinum 135 | montel mirrors | 2011-01-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 2.49 | 84.27 | 96.9 | 0.096 | 0.096 | 10.6 | 4 | 18970 | 18970 |
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 | 2.49 | 2.58 | 86.9 | 0.238 | 0.238 | 3.2 | 10.6 | 1756 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | model generated using binary complex, PDB entry 3RBV | 2.49 | 65 | 18010 | 18010 | 959 | 97.04 | 0.19192 | 0.18883 | 0.25299 | RANDOM | 17.118 |
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] | |
-0.39 | 0.18 | 0.21 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.872 |
r_dihedral_angle_4_deg | 20.421 |
r_dihedral_angle_3_deg | 15.376 |
r_dihedral_angle_1_deg | 6.79 |
r_scangle_it | 5.637 |
r_scbond_it | 3.755 |
r_angle_refined_deg | 2.275 |
r_mcangle_it | 2.13 |
r_mcbond_it | 1.166 |
r_chiral_restr | 0.135 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2478 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms | 117 |
Software
Software | |
---|---|
Software Name | Purpose |
PROTEUM PLUS | data collection |
PHASER | phasing |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |