6JEX
K4U bound crystal peptide deformylase from Acinetobacter baumanii
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6JER |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 8.5 | 287 | 0.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) PEGMME, 15% (w/v) PEG 20000, 0.1 M Tris (base)/ Bicine pH 8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.176 | α = 90 |
b = 40.176 | β = 90 |
c = 187.645 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | ADSC QUANTUM 315r | 2017-10-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 5C (4A) | 0.97950 | PAL/PLS | 5C (4A) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.1 | 50 | 98.2 | 0.105 | 0.129 | 0.075 | 21.8 | 2.8 | 19227 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.1 | 2.14 | 100 | 0.316 | 0.389 | 0.225 | 0.83 | 2.8 |
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 | 6JER | 2.11 | 49.99 | 18121 | 1053 | 98.2 | 0.2011 | 0.1971 | 0.2721 | RANDOM | 36.625 |
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 |
r_dihedral_angle_2_deg | 38.108 |
r_dihedral_angle_4_deg | 22.099 |
r_dihedral_angle_3_deg | 18.743 |
r_dihedral_angle_1_deg | 6.56 |
r_angle_refined_deg | 1.894 |
r_angle_other_deg | 1.184 |
r_chiral_restr | 0.125 |
r_bond_refined_d | 0.016 |
r_gen_planes_refined | 0.011 |
r_gen_planes_other | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2584 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
MOLREP | phasing |