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Neutrophil Gelatinase-associated Lipocalin is a Novel Bacteriostatic Agent that Interferes with Siderophore-mediated Iron Acquisition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QQS PDB ENTRY 1QQS
Crystallization Crystalization Experiments 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 Matthews coefficient Solvent content 3.07 59.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.078 α = 90 b = 115.078 β = 90 c = 115.221 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment 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 ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
Data Collection Overall 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 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 (Depositor) R-Free (Depositor) 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 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 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
RMS Deviations 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 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.023 r_gen_planes_refined 0.017 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 Atoms Number Protein Atoms 4133 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 124
Software Software Software Name Purpose DENZO data reduction HKL-2000 data reduction EPMR phasing REFMAC refinement HKL-2000 data scaling