1L6M
Neutrophil Gelatinase-associated Lipocalin is a Novel Bacteriostatic Agent that Interferes with Siderophore-mediated Iron Acquisition
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QQS | PDB ENTRY 1QQS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 298 | PEG 8000, ammonium sulphate, glycerol, PIPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 59.93 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 115.078 | ¦Á = 90 |
b = 115.078 | ¦Â = 90 |
c = 115.221 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 41 21 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 | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.4 | 19.76 | 96.5 | 0.057 | 29626 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 1QQS | 2.4 | 19.76 | 30746 | 28156 | 1470 | 96.52 | 0.23376 | 0.23248 | 0.25818 | RANDOM | 38.184 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.04 | 0.04 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 22.522 |
r_scangle_it | 3.58 |
r_dihedral_angle_1_deg | 2.728 |
r_angle_refined_deg | 2.236 |
r_scbond_it | 2.113 |
r_mcangle_it | 1.911 |
r_mcbond_it | 1.023 |
r_nbd_refined | 0.257 |
r_symmetry_vdw_refined | 0.215 |
r_xyhbond_nbd_refined | 0.134 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4133 |
Nucleic Acid Atoms | |
Solvent Atoms | 61 |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
HKL-2000 | data reduction |
EPMR | phasing |
REFMAC | refinement |
HKL-2000 | data scaling |