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Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A 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 65.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.508 α = 90 b = 81.76 β = 130.322 c = 111.794 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) Rrim I (All) 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 2.7 67.115 97.61 0.2 0.42 0.17 0.89 2.7 3.1 29165
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 2.7 2.77 98.31 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 2.7 67.115 28469 1430 97.614 0.244 0.2408 0.2447 0.3142 0.3093 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] 0.038 -0.039 -0.049 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.325 r_dihedral_angle_3_deg 20.619 r_dihedral_angle_4_deg 20.082 r_lrange_other 13.729 r_lrange_it 13.725 r_mcangle_it 9.494 r_mcangle_other 9.493 r_scangle_it 8.845 r_scangle_other 8.844 r_dihedral_angle_1_deg 7.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.325 r_dihedral_angle_3_deg 20.619 r_dihedral_angle_4_deg 20.082 r_lrange_other 13.729 r_lrange_it 13.725 r_mcangle_it 9.494 r_mcangle_other 9.493 r_scangle_it 8.845 r_scangle_other 8.844 r_dihedral_angle_1_deg 7.351 r_mcbond_other 5.991 r_mcbond_it 5.99 r_scbond_it 5.43 r_scbond_other 5.429 r_angle_refined_deg 1.605 r_angle_other_deg 1.16 r_symmetry_nbd_refined 0.455 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.216 r_nbd_other 0.205 r_symmetry_nbd_other 0.203 r_xyhbond_nbd_refined 0.2 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_other 0.141 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5314 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 219
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing