5DVY
2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | Protein: 12.4 mg/ml, 0.01M Tris-HCL (pH 8.3), Screen: Classics II (A3), 0.1M Bis-Tris (pH 5.5), 2M Ammonium sulfate, Cryo: 25% Sucrose, 2M Ammonium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.82 | 78.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 193.162 | α = 90 |
b = 193.162 | β = 90 |
c = 156.478 | γ = 120 |
Symmetry | |
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Space Group | P 63 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 | MARMOSAIC 225 mm CCD | 2015-03-09 | 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) | 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 | 2.95 | 30 | 99.8 | 0.13 | 0.13 | 23.7 | 13.2 | 36548 | -3 | 68.2 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.95 | 3 | 100 | 0.69 | 4 | 13.5 |
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 | 2.95 | 29.91 | 34772 | 1762 | 99.45 | 0.15437 | 0.1527 | 0.18678 | RANDOM | 62.27 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.11 | -0.06 | -0.11 | 0.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.647 |
r_dihedral_angle_4_deg | 10.942 |
r_dihedral_angle_3_deg | 9.395 |
r_long_range_B_refined | 7.915 |
r_long_range_B_other | 7.915 |
r_scangle_other | 5.952 |
r_scbond_it | 4.215 |
r_scbond_other | 4.194 |
r_mcangle_it | 3.758 |
r_mcangle_other | 3.757 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4898 |
Nucleic Acid Atoms | |
Solvent Atoms | 243 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |
BLU-MAX | data collection |