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The crystal structure of diferric porcine serum transferrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.39 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.77 α = 90 b = 44.89 β = 105.39 c = 78.86 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 277 IMAGE PLATE MAR scanner 300 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.5 SRS PX9.5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 23.3 96 0.073 15.7 3.6 41503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.2 97.4 0.123 8.1 3.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 0TFD 2.15 30 38011 2001 96 0.136 0.1459 0.182 0.1902 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.593 r_scbond_it 3.39 r_mcangle_it 2.424 r_angle_other_deg 1.961 r_dihedral_angle_3_deg 1.364 r_mcbond_it 1.313 r_symmetry_vdw_other 0.389 r_symmetry_hbond_refined 0.245 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.224
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.593 r_scbond_it 3.39 r_mcangle_it 2.424 r_angle_other_deg 1.961 r_dihedral_angle_3_deg 1.364 r_mcbond_it 1.313 r_symmetry_vdw_other 0.389 r_symmetry_hbond_refined 0.245 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.224 r_nbd_other 0.212 r_nbtor_other 0.192 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.125 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5233 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction XDISP data reduction SCALEPACK data scaling AMoRE phasing