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Crystal Structure of the complex of C-lobe of lactoferrin with indole acetic acid at 2.68 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 0.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.234 α = 90 b = 50.396 β = 107.7 c = 65.893 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 IMAGE PLATE MARRESEARCH MIRROR 2010-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.541
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 2.68 63.25 98.2 9.8 11266 10731
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 2.68 2.78 99.8
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 3IB1 2.68 63.24 10309 10309 535 99.59 0.176 0.17456 0.17214 0.1764 0.22243 0.2253 RANDOM 39.988
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] 0.91 -1.33 -1.44 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.795 r_dihedral_angle_3_deg 17.971 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_1_deg 6.097 r_scangle_it 3.793 r_scbond_it 2.296 r_angle_refined_deg 2.075 r_mcangle_it 1.715 r_mcbond_it 0.963 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.795 r_dihedral_angle_3_deg 17.971 r_dihedral_angle_4_deg 16.086 r_dihedral_angle_1_deg 6.097 r_scangle_it 3.793 r_scbond_it 2.296 r_angle_refined_deg 2.075 r_mcangle_it 1.715 r_mcbond_it 0.963 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.307 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.161 r_metal_ion_refined 0.128 r_chiral_restr 0.092 r_symmetry_metal_ion_refined 0.06 r_bond_refined_d 0.02 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 95
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling