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Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 A 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 3.55 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.781 α = 90 b = 81.703 β = 129.857 c = 111.694 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 MASSIF-1 0.96546 ESRF MASSIF-1
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 2.277 76.7 98.8 0.03 0.97 17.6 3 48821
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 2.277 2.31 99.8 0.44 0.94 2.9 3.2
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 FREE R-VALUE 1BLF 2.277 76.7 48241 2465 98.814 0.214 0.2126 0.2127 0.2469 0.2471 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] 0.788 0.92 -8.288 2.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.295 r_dihedral_angle_4_deg 20.238 r_dihedral_angle_3_deg 18.013 r_lrange_other 15.265 r_lrange_it 15.244 r_scangle_other 10.378 r_scangle_it 10.376 r_mcangle_it 9.995 r_mcangle_other 9.993 r_dihedral_angle_1_deg 7.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.295 r_dihedral_angle_4_deg 20.238 r_dihedral_angle_3_deg 18.013 r_lrange_other 15.265 r_lrange_it 15.244 r_scangle_other 10.378 r_scangle_it 10.376 r_mcangle_it 9.995 r_mcangle_other 9.993 r_dihedral_angle_1_deg 7.46 r_mcbond_it 7.176 r_mcbond_other 7.169 r_scbond_other 7.116 r_scbond_it 7.114 r_angle_other_deg 2.518 r_angle_refined_deg 1.607 r_nbd_other 0.271 r_symmetry_xyhbond_nbd_other 0.231 r_symmetry_nbd_other 0.23 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.198 r_xyhbond_nbd_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.163 r_ncsr_local_group_1 0.082 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.066 r_bond_other_d 0.036 r_metal_ion_refined 0.012 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5314 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing