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crystal structure of Cd(II)Ca(II)Mg(II)-bound human calprotectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QUV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M MgCl2, 0.1M Hepes pH7.0, 15% PEG4,000
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.452 α = 90 b = 78.23 β = 90 c = 223.157 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS4 X 4M 2025-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-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 1.85 223.09 99 0.096 13.5 8.9 85455
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 1.85 1.89 1.03
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.854 73.935 85249 4355 98.698 0.17 0.1671 0.1773 0.2192 0.2272 29.031
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] 0.472 -0.067 -0.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.16 r_dihedral_angle_3_deg 13.154 r_lrange_it 7.522 r_dihedral_angle_2_deg 7.462 r_lrange_other 7.412 r_dihedral_angle_1_deg 5.868 r_scangle_it 5.718 r_scangle_other 5.717 r_scbond_it 3.835 r_scbond_other 3.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.16 r_dihedral_angle_3_deg 13.154 r_lrange_it 7.522 r_dihedral_angle_2_deg 7.462 r_lrange_other 7.412 r_dihedral_angle_1_deg 5.868 r_scangle_it 5.718 r_scangle_other 5.717 r_scbond_it 3.835 r_scbond_other 3.835 r_mcangle_it 3.825 r_mcangle_other 3.825 r_mcbond_it 2.784 r_mcbond_other 2.778 r_angle_refined_deg 1.623 r_angle_other_deg 0.571 r_metal_ion_refined 0.319 r_symmetry_xyhbond_nbd_refined 0.271 r_nbd_other 0.266 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.206 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.181 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6474 Nucleic Acid Atoms Solvent Atoms 825 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing