5K8C
X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 3RF7 | PDB entry 3RF7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 277 | 7-9% PEG-8000, 100 mM homopipes, 1 M tetramethylammonium chloride |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.16 | 61.03 |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 107.594 | ¦Á = 90 |
b = 107.594 | ¦Â = 90 |
c = 149.861 | ¦Ã = 120 |
Symmetry | |
---|---|
Space Group | P 63 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 | 2015-06-15 | 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 | 1.85 | 93.18 | 99.3 | 0.083 | 0.083 | 11.2 | 7.6 | 44036 |
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 | 1.85 | 1.95 | 99 | 0.399 | 3.1 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3RF7 | 1.85 | 93.18 | 41818 | 2218 | 99.34 | 0.18052 | 0.17851 | 0.21811 | RANDOM | 19.154 |
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] | |
0.48 | 0.24 | 0.48 | -1.57 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.577 |
r_dihedral_angle_4_deg | 21.318 |
r_dihedral_angle_3_deg | 14.761 |
r_dihedral_angle_1_deg | 6.559 |
r_long_range_B_refined | 6.248 |
r_long_range_B_other | 6.247 |
r_scangle_other | 4.258 |
r_scbond_it | 2.871 |
r_scbond_other | 2.865 |
r_mcangle_other | 2.423 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2774 |
Nucleic Acid Atoms | |
Solvent Atoms | 438 |
Heterogen Atoms | 61 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |
PHASER | phasing |