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Crystal Structure of the Europium-bound Lanmodulin from Ancylobacter novellus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 8 294 0.1 M Tris pH 8.0, 0.1 M KBr, 40% PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.82 31.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.749 α = 90 b = 50.672 β = 97.36 c = 45.179 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M 2026-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.5 44.81 98.96 0.99 7 1.9 27616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 0.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION SAD NONE 1.5 44.81 1.38 27614 1355 98.95 0.1564 0.1549 0.1553 0.1861 0.1858
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.402 f_angle_d 0.972 f_chiral_restr 0.09 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1690 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling CRANK2 phasing