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Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam-hopo2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6M PDB ENTRY 1L6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.084 α = 90 b = 114.084 β = 90 c = 118.422 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 210 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 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 2.19 50 100 0.094 24.29 10.5 52918 40660
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) 2.19 2.28 100 0.43 6.6 10.6 3989
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 Used previously-determined structure THROUGHOUT PDB ENTRY 1L6M 2.19 46.93 36725 3868 99.82 0.24482 0.24244 0.2414 0.26785 0.2642 Used same set as previously-determined structure 31.102
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] -0.16 -0.16 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.577 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 13.98 r_dihedral_angle_1_deg 5.073 r_scangle_it 1.312 r_angle_refined_deg 1.038 r_mcangle_it 0.798 r_angle_other_deg 0.766 r_scbond_it 0.757 r_mcbond_it 0.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.577 r_dihedral_angle_4_deg 16.884 r_dihedral_angle_3_deg 13.98 r_dihedral_angle_1_deg 5.073 r_scangle_it 1.312 r_angle_refined_deg 1.038 r_mcangle_it 0.798 r_angle_other_deg 0.766 r_scbond_it 0.757 r_mcbond_it 0.424 r_chiral_restr 0.055 r_mcbond_other 0.041 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4008 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 239
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing