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Crystal structure of Neutrophil gelatinase-associated lipocalin NGAL (C87S mutant) in complex with fragment 1026, phenylurea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TF6 PDB entry 3TF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 HosaA.18070.a protein at 10 mg/mL against 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate with 15% glycerol as cryo-protectant, crystal tracking ID 224571a10, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.35 α = 90 b = 115.35 β = 90 c = 119.89 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 MARMOSAIC 300 mm CCD 2011-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03322 APS 23-ID-B
Data Collection Overall 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 2.45 50 99.7 0.121 11.49 6.2 30343 30248 -3 37.733
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 2.45 2.51 99.8 0.543 3.64 6.4 2193
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3TF6 2.45 50 30248 1532 99.68 0.1891 0.1872 0.1865 0.2247 0.2243 RANDOM 31.3309
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] -0.12 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.031 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 16.057 r_dihedral_angle_1_deg 6.401 r_angle_refined_deg 1.504 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4067 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 101
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing