7T35
Crystal Structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC from Klebsiella pneumoniae subsp. pneumoniae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2R8E | pdb entry 2r8eA as per Morda |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 287 | RigakuReagents JCSG+ screen, condition a1: 50% (v/v) PEG 400 100 mM Sodium acetate/ Acetic acid pH 4.5 200 mM Lithium sulfate: KlpnC.017337.a.B1.PW39027 at 23mg/ml: tray 322405a1: cryo: direct: puck kzu0-2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.42 | α = 90 |
b = 92.42 | β = 90 |
c = 87.83 | γ = 90 |
Symmetry | |
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Space Group | I 4 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-300 | Beryllium Lenses | 2021-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.65 | 50 | 99.9 | 0.047 | 0.049 | 1 | 34.65 | 14.07 | 5801 | 71.572 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.65 | 2.72 | 100 | 0.568 | 0.589 | 0.957 | 5.01 | 14.694 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | pdb entry 2r8eA as per Morda | 2.65 | 32.68 | 1.36 | 5794 | 612 | 99.93 | 0.2249 | 0.2201 | 0.2636 | 0 | 83.92 |
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 | 13.703 |
f_angle_d | 0.6922 |
f_chiral_restr | 0.0453 |
f_plane_restr | 0.0053 |
f_bond_d | 0.0049 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1123 |
Nucleic Acid Atoms | |
Solvent Atoms | 3 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MoRDa | phasing |
PHENIX | model building |
Coot | model building |