2CBG
Crystal structure of the PMSF-inhibited thioesterase domain of the fengycin biosynthesis cluster
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JMK | PDB ENTRY 1JMK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.6 | 0.2 M NH4 ACETATE, 0.1 M NA CITRATE (PH 5.6), 22.5 % PEG 8000, 10 MG/ML PROTEIN |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 53 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 72.354 | ¦Á = 90 |
b = 72.354 | ¦Â = 90 |
c = 96.333 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 |
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 | IMAGE PLATE | MARRESEARCH | OSMIC MIRRORS | 2003-10-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | ENRAF-NONIUS FR591 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.5 | 24 | 91.6 | 0.08 | 20.2 | 3.76 | 9190 | -3 | 41.6 |
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 | 2.5 | 2.56 | 54.9 | 0.22 | 4.4 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1JMK | 2.5 | 24 | 8690 | 489 | 92.2 | 0.166 | 0.162 | 0.237 | RANDOM | 37.4 |
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] | |
0.53 | 0.27 | 0.53 | -0.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 8.721 |
r_scangle_it | 6.856 |
r_scbond_it | 4.495 |
r_mcangle_it | 2.982 |
r_angle_refined_deg | 2.589 |
r_mcbond_it | 1.608 |
r_nbd_refined | 0.238 |
r_symmetry_vdw_refined | 0.231 |
r_symmetry_hbond_refined | 0.231 |
r_xyhbond_nbd_refined | 0.198 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1665 |
Nucleic Acid Atoms | |
Solvent Atoms | 75 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |