5OAU
Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae
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 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.57 | 65.51 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 100.26 | ¦Á = 90 |
b = 100.26 | ¦Â = 90 |
c = 189.81 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | 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 | 2.67 | 34.78 | 99.3 | 0.1 | 0.09 | 7.5 | 3.5 | 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 | 2.67 | 2.8 | 99.1 | 0.57 | 0.48 | 1.7 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2.67 | 34.78 | 30573 | 1506 | 99.88 | 0.17588 | 0.17345 | 0.22531 | RANDOM | 62.804 |
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] | |
-0.05 | -0.03 | -0.05 | 0.17 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.587 |
r_dihedral_angle_3_deg | 15.943 |
r_dihedral_angle_4_deg | 14.903 |
r_long_range_B_refined | 12.249 |
r_long_range_B_other | 12.247 |
r_scangle_other | 7.953 |
r_mcangle_it | 7.871 |
r_mcangle_other | 7.87 |
r_dihedral_angle_1_deg | 7.28 |
r_scbond_it | 5.464 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5131 |
Nucleic Acid Atoms | |
Solvent Atoms | 229 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data scaling |
XDS | data reduction |
MOLREP | phasing |