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Crystal structure of K206E mutant of N-lobe human transferrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A8E N-lobe human transferrin, PDB code 1A8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 Protein: 35mg/ml, 0.1M ammonium bicrbonate. Well: 18% PEG3350, 0.2M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.173 α = 90 b = 57.317 β = 90 c = 135.583 γ = 90
Symmetry Space Group P 21 21 21
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 2005-06-07 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 2.6 22.7 98.5 0.139 9 3.3 10917 10917 32.58
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) 2.6 2.74 100 0.377 3 3.2 1576
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 (All) 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 N-lobe human transferrin, PDB code 1A8E 2.6 21.02 10358 10358 521 97.99 0.216 0.216 0.213 0.2106 0.269 0.2628 RANDOM 15.196
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] 0.02 0.07 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_1_deg 5.392 r_scangle_it 2.116 r_angle_refined_deg 1.273 r_scbond_it 1.257 r_mcangle_it 0.868 r_mcbond_it 0.46 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.633 r_dihedral_angle_4_deg 20.708 r_dihedral_angle_3_deg 16.26 r_dihedral_angle_1_deg 5.392 r_scangle_it 2.116 r_angle_refined_deg 1.273 r_scbond_it 1.257 r_mcangle_it 0.868 r_mcbond_it 0.46 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.087 r_metal_ion_refined 0.045 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2551 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 6
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing