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Crystal structure of the C-lobe of lactoferrin produced by limited proteolysis using pepsin at 2.74A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBC
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 3.52 65.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.759 α = 90 b = 81.554 β = 129.949 c = 111.364 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 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) Rrim 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 2.74 76.85 97.5 0.06 0.07 0.99 10.2 2.9 27187
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.79 0.03 0.04 0.99
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 5HBC 2.743 76.846 27050 1361 96.995 0.242 0.2388 0.243 0.2984 0.3008 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] 2.535 2.636 -13.1 2.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.207 r_dihedral_angle_4_deg 22.618 r_dihedral_angle_3_deg 21.628 r_lrange_it 15.116 r_lrange_other 15.114 r_mcangle_it 11.547 r_mcangle_other 11.545 r_scangle_it 11.027 r_scangle_other 11.026 r_mcbond_it 7.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.207 r_dihedral_angle_4_deg 22.618 r_dihedral_angle_3_deg 21.628 r_lrange_it 15.116 r_lrange_other 15.114 r_mcangle_it 11.547 r_mcangle_other 11.545 r_scangle_it 11.027 r_scangle_other 11.026 r_mcbond_it 7.75 r_mcbond_other 7.749 r_scbond_it 7.218 r_scbond_other 7.218 r_dihedral_angle_1_deg 6.843 r_angle_refined_deg 1.681 r_angle_other_deg 1.199 r_nbd_other 0.299 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.214 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_refined 0.202 r_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.062 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5316 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing