7Q4S
Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87, apo form.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5NM7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9.5 | 294 | 20% (w/v) PEG 8000, 0.1 M CHES-NaOH, 20 mM Tris-HCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.247 | α = 90 |
b = 68.085 | β = 90 |
c = 93.1 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2019-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALBA BEAMLINE XALOC | 0.97926 | ALBA | XALOC |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.5 | 59.25 | 99.7 | 0.183 | 0.202 | 0.083 | 0.991 | 6 | 5.7 | 13640 | 31.796 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.5 | 2.6 | 99.1 | 0.99 | 1.087 | 0.444 | 0.86 | 2.1 | 5.7 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5NM7 | 2.5 | 55.018 | 13599 | 658 | 99.743 | 0.225 | 0.2222 | 0.2779 | 56.402 |
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] | |
-3.567 | -2.533 | 6.1 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.684 |
r_dihedral_angle_4_deg | 17.027 |
r_dihedral_angle_3_deg | 11.734 |
r_dihedral_angle_1_deg | 4.813 |
r_lrange_it | 4.214 |
r_lrange_other | 4.214 |
r_mcangle_it | 2.011 |
r_mcangle_other | 2.011 |
r_scangle_it | 1.533 |
r_scangle_other | 1.533 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2964 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 39 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
MOLREP | phasing |