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Crystal Structure of human transferrin receptor in complex with a cystine-dense peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DE4 pdbid 1de4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 PEG 6000, Mes
Crystal Properties Matthews coefficient Solvent content 3.36 63.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.601 α = 90 b = 145.5 β = 90.02 c = 133.494 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 2018-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.979 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 50 99.8 0.086 0.103 0.056 8.3 3.3 166017
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 99.9 0.693 0.824 0.441 0.664 3.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdbid 1de4 1.85 50.01 157641 8375 99.43 0.16405 0.16278 0.1743 0.18714 0.196 RANDOM 26.399
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] -0.6 -0.17 0.57 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.63 r_dihedral_angle_4_deg 20.643 r_dihedral_angle_3_deg 13.644 r_dihedral_angle_1_deg 6.84 r_long_range_B_other 6.642 r_long_range_B_refined 6.641 r_scangle_other 5.473 r_scbond_it 3.929 r_scbond_other 3.929 r_mcangle_it 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.63 r_dihedral_angle_4_deg 20.643 r_dihedral_angle_3_deg 13.644 r_dihedral_angle_1_deg 6.84 r_long_range_B_other 6.642 r_long_range_B_refined 6.641 r_scangle_other 5.473 r_scbond_it 3.929 r_scbond_other 3.929 r_mcangle_it 2.842 r_mcangle_other 2.842 r_mcbond_it 2.187 r_mcbond_other 2.187 r_angle_refined_deg 1.611 r_angle_other_deg 0.85 r_chiral_restr 0.199 r_gen_planes_refined 0.018 r_bond_refined_d 0.016 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10156 Nucleic Acid Atoms Solvent Atoms 782 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction