7L6Z
Crystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (PpiB) Streptococcus pneumoniae R6
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 292 | Protein: 5.0 mg/ml, 0.01M Tris pH 8.3;Screen: PACT (B8), 0.2M Ammonium chloride, 0.1M MES pH 6.0, 20% (w/v) PEG6000. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.432 | α = 90 |
b = 156.529 | β = 117.18 |
c = 90.535 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | MARMOSAIC 300 mm CCD | Be | 2019-07-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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) | R Sym I (Observed) | Rrim I (All) | 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 | 1.88 | 30 | 99.1 | 0.087 | 0.087 | 0.098 | 0.045 | 16.6 | 4.4 | 175455 | -3 | 27.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.88 | 1.91 | 99.1 | 0.758 | 0.758 | 0.857 | 0.393 | 0.725 | 2.3 | 4.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.88 | 29.97 | 166357 | 9021 | 98.92 | 0.1748 | 0.1728 | 0.2124 | RANDOM | 34.069 |
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] | |
-0.64 | 0.9 | -1.06 | 0.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.448 |
r_dihedral_angle_4_deg | 10.811 |
r_dihedral_angle_3_deg | 8.785 |
r_dihedral_angle_1_deg | 3.242 |
r_angle_refined_deg | 1.329 |
r_angle_other_deg | 0.356 |
r_chiral_restr | 0.064 |
r_gen_planes_refined | 0.054 |
r_gen_planes_other | 0.052 |
r_bond_refined_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16640 |
Nucleic Acid Atoms | |
Solvent Atoms | 1551 |
Heterogen Atoms | 108 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
HKL-3000 | phasing |