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)
TypeSourceAccession CodeDetails
experimental modelPDB 1QQSPDB ENTRY 1QQS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17298PEG 8000, ammonium sulphate, glycerol, PIPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
3.0759.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.078α = 90
b = 115.078β = 90
c = 115.221γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.419.7696.50.05729626

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QQS2.419.763074628156147096.520.233760.232480.25818RANDOM38.184
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]
0.040.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.522
r_scangle_it3.58
r_dihedral_angle_1_deg2.728
r_angle_refined_deg2.236
r_scbond_it2.113
r_mcangle_it1.911
r_mcbond_it1.023
r_nbd_refined0.257
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg22.522
r_scangle_it3.58
r_dihedral_angle_1_deg2.728
r_angle_refined_deg2.236
r_scbond_it2.113
r_mcangle_it1.911
r_mcbond_it1.023
r_nbd_refined0.257
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.092
r_bond_refined_d0.023
r_gen_planes_refined0.017
r_bond_other_d
r_angle_other_deg
r_chiral_restr
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4133
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms124

Software

Software
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
EPMRphasing
REFMACrefinement
HKL-2000data scaling