☰ Navigation Tabs
Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-BisHaCam
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 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.428 α = 90 b = 115.428 β = 90 c = 119.289 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 2.8 50 97.4 0.078 12.6 5.5 19821
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) 2.8 2.9 96 0.24 4 4.8 1909
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 2.8 48.17 17936 1842 97.23 0.23287 0.2276 0.2297 0.28506 0.2833 Used same set as previously-determined structure 28.198
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] 0.2 0.2 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_3_deg 16.783 r_dihedral_angle_4_deg 16.081 r_dihedral_angle_1_deg 6.987 r_angle_refined_deg 1.084 r_scangle_it 0.884 r_angle_other_deg 0.84 r_scbond_it 0.526 r_mcangle_it 0.443 r_mcbond_it 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_3_deg 16.783 r_dihedral_angle_4_deg 16.081 r_dihedral_angle_1_deg 6.987 r_angle_refined_deg 1.084 r_scangle_it 0.884 r_angle_other_deg 0.84 r_scbond_it 0.526 r_mcangle_it 0.443 r_mcbond_it 0.236 r_nbd_refined 0.19 r_nbd_other 0.185 r_nbtor_refined 0.18 r_symmetry_vdw_other 0.172 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.137 r_metal_ion_refined 0.128 r_xyhbond_nbd_refined 0.116 r_nbtor_other 0.079 r_chiral_restr 0.062 r_mcbond_other 0.023 r_bond_other_d 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4062 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 198
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing