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Intermediate structure of iron-saturated C-lobe of bovine lactoferrin at 2.79 Angstrom resolution indicates the softening of iron coordination
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 300 0.05M HEPES, 20% PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.58 65.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.654 α = 90 b = 82.58 β = 128.08 c = 107.694 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 80 CCD MARRESEARCH 2014-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.788 39.45 99.2 16 4.1 27307 27307
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.788 2.86
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4NED 2.79 39.45 25919 1369 98.47 0.20948 0.2061 0.2727 0.2512 RANDOM 67.422
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] -0.27 0.18 -3.15 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.204 r_dihedral_angle_4_deg 21.866 r_dihedral_angle_3_deg 20.111 r_long_range_B_refined 10.155 r_long_range_B_other 10.153 r_scangle_other 7.626 r_mcangle_it 7.446 r_mcangle_other 7.445 r_dihedral_angle_1_deg 7.388 r_scbond_it 5.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.204 r_dihedral_angle_4_deg 21.866 r_dihedral_angle_3_deg 20.111 r_long_range_B_refined 10.155 r_long_range_B_other 10.153 r_scangle_other 7.626 r_mcangle_it 7.446 r_mcangle_other 7.445 r_dihedral_angle_1_deg 7.388 r_scbond_it 5.065 r_scbond_other 5.032 r_mcbond_it 4.844 r_mcbond_other 4.844 r_angle_other_deg 3.683 r_angle_refined_deg 1.857 r_chiral_restr 0.107 r_gen_planes_other 0.025 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 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 5316 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing