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Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other the structure was solved using the molecular replacement method using the auto-MR tool employing MrBUMP with MorDa within the CCP4 cloud server. the initial search model obtained was subjected to several refinement cycles to obtain the final solution.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1M Sodium acetate trihydrate (pH 4.6), 0.2M ammonium sulfate, 25% w/v PEG 2000
Crystal Properties Matthews coefficient Solvent content 2.6 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.684 α = 90 b = 139.06 β = 90 c = 120.741 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 9M 2023-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.82 47.583 99.6 0.155 0.096 0.995 8.3 6.7 19057 72.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.82 2.97 99.8 1.497 0.912 0.535 1.2 7
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 2.82 47.583 19046 371 99.343 0.213 0.2114 0.2156 0.2686 0.27 79.726
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] 3.317 -3.681 0.363
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 15.334 r_lrange_it 15.333 r_dihedral_angle_3_deg 14.79 r_dihedral_angle_6_deg 13.386 r_dihedral_angle_2_deg 10.706 r_scangle_it 9.47 r_scangle_other 9.461 r_mcangle_it 8.078 r_mcangle_other 8.077 r_dihedral_angle_1_deg 7.617
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 15.334 r_lrange_it 15.333 r_dihedral_angle_3_deg 14.79 r_dihedral_angle_6_deg 13.386 r_dihedral_angle_2_deg 10.706 r_scangle_it 9.47 r_scangle_other 9.461 r_mcangle_it 8.078 r_mcangle_other 8.077 r_dihedral_angle_1_deg 7.617 r_scbond_it 5.777 r_scbond_other 5.766 r_mcbond_it 5.065 r_mcbond_other 5.065 r_angle_other_deg 1.897 r_angle_refined_deg 1.506 r_nbd_refined 0.236 r_symmetry_nbd_other 0.222 r_nbd_other 0.186 r_symmetry_nbd_refined 0.181 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.173 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.135 r_symmetry_nbtor_other 0.102 r_symmetry_xyhbond_nbd_other 0.031 r_gen_planes_other 0.024 r_gen_planes_refined 0.012 r_bond_refined_d 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5182 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 333
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building