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Crystal structure of K206E/K296E mutant of the N-terminal half molecule of human transferrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A8E Wild type transferrin. PDB entry code 1A8E.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 291 Protein: 35mg/ml, 0.1M ammonium bicarbonate. Well: 20% PEG 3350, 0.2 M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.462 α = 90 b = 97.897 β = 90.01 c = 208.953 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 110 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2006-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.8 48 98.5 0.074 16.4 3.3 83306 83306
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 2.8 2.95 98.8 0.406 3.2 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 Wild type transferrin. PDB entry code 1A8E. 2.8 29.76 82144 78012 4132 97.33 0.23109 0.22961 0.2236 0.25885 0.2244 RANDOM 57.888
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] 0.14 0.2 -0.28 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_4_deg 18.612 r_dihedral_angle_3_deg 17.55 r_dihedral_angle_1_deg 5.993 r_scangle_it 2.313 r_angle_refined_deg 1.323 r_scbond_it 1.299 r_mcangle_it 0.854 r_mcbond_it 0.44 r_symmetry_vdw_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.16 r_dihedral_angle_4_deg 18.612 r_dihedral_angle_3_deg 17.55 r_dihedral_angle_1_deg 5.993 r_scangle_it 2.313 r_angle_refined_deg 1.323 r_scbond_it 1.299 r_mcangle_it 0.854 r_mcbond_it 0.44 r_symmetry_vdw_refined 0.317 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.093 r_metal_ion_refined 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22950 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 45
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling