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Crystal structure of iron-saturated C-terminal half of lactoferrin produced proteolytically using pepsin at 2.32A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BLF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 Magnesium acetate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.47 64.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.67 α = 90 b = 82.027 β = 129.624 c = 112.137 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M-F MIRROR 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9655 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.32 86.38 98.8 0.036 0.99 15.1 3 47113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.38 99.7 0.47 0.91 2.3 2.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BLF 2.322 77.748 46529 2275 98.75 0.205 0.2029 0.2487 0.2646 70
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] 4.514 1.272 -7.93 0.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_dihedral_angle_4_deg 21.809 r_dihedral_angle_3_deg 18.796 r_lrange_it 12.414 r_lrange_other 12.413 r_scangle_it 10.156 r_scangle_other 10.155 r_mcangle_it 8.763 r_mcangle_other 8.762 r_dihedral_angle_1_deg 7.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_dihedral_angle_4_deg 21.809 r_dihedral_angle_3_deg 18.796 r_lrange_it 12.414 r_lrange_other 12.413 r_scangle_it 10.156 r_scangle_other 10.155 r_mcangle_it 8.763 r_mcangle_other 8.762 r_dihedral_angle_1_deg 7.744 r_scbond_it 6.897 r_scbond_other 6.896 r_mcbond_it 6.212 r_mcbond_other 6.206 r_angle_refined_deg 1.706 r_angle_other_deg 1.257 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_other 0.223 r_nbd_refined 0.206 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.161 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.145 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5314 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing