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Crystal Structure of the complex of C-lobe of lactoferrin with isopropylamino-3-(1-naphthyloxy)propan-2-ol at 2.38 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DWA
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 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.107 α = 90 b = 50.248 β = 107.82 c = 65.654 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 2010-04-05 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) R Sym 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 2.38 62.5 97.4 0.094 9.1 15943 15943
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.38 2.44 94.7 0.448 1.9
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 2DWA 2.38 62.5 15519 14746 773 97.42 0.176 0.17417 0.17148 0.1723 0.21142 0.2267 RANDOM 34.214
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] 0.32 -1.33 -0.6 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.053 r_dihedral_angle_4_deg 19.539 r_dihedral_angle_3_deg 17.331 r_dihedral_angle_1_deg 6.63 r_scangle_it 3.644 r_scbond_it 2.1 r_mcangle_it 1.516 r_angle_refined_deg 1.428 r_mcbond_it 0.844 r_symmetry_hbond_refined 0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.053 r_dihedral_angle_4_deg 19.539 r_dihedral_angle_3_deg 17.331 r_dihedral_angle_1_deg 6.63 r_scangle_it 3.644 r_scbond_it 2.1 r_mcangle_it 1.516 r_angle_refined_deg 1.428 r_mcbond_it 0.844 r_symmetry_hbond_refined 0.384 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.303 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.133 r_symmetry_metal_ion_refined 0.131 r_chiral_restr 0.086 r_metal_ion_refined 0.032 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 126
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling