7U4H
Crystal Structure of Penicillin-binding protein 1A (Pbp1a) from Chlamydia trachomatis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2JCH | MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B |
experimental model | PDB | 5U2G | MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B |
experimental model | PDB | 3VMA | MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B |
experimental model | PDB | 4OON | MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 287 | RigakuReagents Wizard3/4 screen condition B8: 100mM HEPES/NaOH pH 7.0, 10% (w/V) PEG 8000: ChtrB.19241.a.D11.PD228392 at 15.5mg/ml + 1mM imipenem: tray: 313782 b8: cryo: 25% EG: puck HIO1-1. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 175.79 | α = 90 |
b = 175.79 | β = 90 |
c = 339.7 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 | 2020-07-02 | 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) | 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 | 3.1 | 50 | 99.8 | 0.112 | 0.128 | 0.995 | 11.77 | 4.35 | 36840 | 49.068 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.1 | 3.18 | 100 | 0.58 | 0.658 | 0.82 | 2.95 | 4.437 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B | 3.1 | 47.6 | 1.35 | 36832 | 2016 | 99.8 | 0.1936 | 0.1923 | 0.2159 | 61.92 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.9451 |
f_angle_d | 0.557 |
f_chiral_restr | 0.0452 |
f_plane_restr | 0.0041 |
f_bond_d | 0.0027 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8883 |
Nucleic Acid Atoms | |
Solvent Atoms | 134 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
MR-Rosetta | phasing |
Coot | model building |