5OJ0
Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with Cefepime
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1K25 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 290 | 2.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.43 | 64.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.547 | α = 90 |
b = 99.547 | β = 90 |
c = 189.66 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 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 | PIXEL | DECTRIS PILATUS 6M | 2015-09-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.97947 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 2.66 | 39.24 | 99.6 | 0.16 | 0.12 | 5.7 | 4.2 | 31872 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.66 | 2.76 | 99.6 | 0.8 | 0.69 | 4.3 |
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 | 1k25 | 2.66 | 39.24 | 30354 | 1621 | 99.93 | 0.17477 | 0.17165 | 0.23143 | RANDOM | 64.555 |
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] | |
-0.14 | -0.07 | -0.14 | 0.46 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.387 |
r_dihedral_angle_3_deg | 19.85 |
r_dihedral_angle_4_deg | 15.192 |
r_long_range_B_other | 13.936 |
r_long_range_B_refined | 13.935 |
r_scangle_other | 10.205 |
r_mcangle_it | 9.637 |
r_mcangle_other | 9.636 |
r_dihedral_angle_1_deg | 8.409 |
r_scbond_it | 7.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5057 |
Nucleic Acid Atoms | |
Solvent Atoms | 212 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
Coot | model building |