5A5F
CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH UMA AND ADP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3UAG | PDB ENTRY 3UAG |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.4 | 4 MG/ML PROTEIN, 1 MM UMA, 5 MM AMP-PNP, 1 MM NAN3, 1 MM DTT, 20 MM HEPES, PH 7.4, 1.8 M NA-MALONATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.37 | 63.55 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 66.44 | ¦Á = 90 |
b = 89.84 | ¦Â = 90 |
c = 108.54 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 CCD | 2008-04-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.9 | 46.46 | 98.2 | 0.06 | 23.75 | 5.4 | 51890 | 3 | 37.009 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.9 | 2.01 | 94.8 | 0.62 | 3.22 | 5.5 |
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 3UAG | 1.9 | 46.47 | 48594 | 2561 | 98.57 | 0.19982 | 0.19809 | 0.23227 | RANDOM | 35.207 |
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] | |
-1.26 | 0.47 | 0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.133 |
r_dihedral_angle_4_deg | 16.115 |
r_dihedral_angle_3_deg | 13.906 |
r_dihedral_angle_1_deg | 7.027 |
r_scbond_it | 3.087 |
r_mcangle_it | 2.622 |
r_mcbond_it | 1.97 |
r_angle_refined_deg | 1.492 |
r_chiral_restr | 0.121 |
r_bond_refined_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3254 |
Nucleic Acid Atoms | |
Solvent Atoms | 269 |
Heterogen Atoms | 90 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |