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Crystal Structure of the Complex of C-lobe of Bovine Lactoferrin with Dextrin at 1.9 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DWA pdb entry 2DWA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.81 α = 90 b = 50.134 β = 107.1 c = 65.545 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 2009-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.91 62.62 96 0.052 7.5 29538 29538
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) 1 1.91 1.96 99.1 0.112 3.1
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 pdb entry 2DWA 1.91 62.62 28296 26864 1432 94.54 0.21068 0.20854 0.215 0.24106 0.2535 RANDOM 24.886
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] 1.04 -0.58 -0.87 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.638 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 16.687 r_dihedral_angle_1_deg 5.85 r_scangle_it 2.473 r_scbond_it 1.59 r_angle_refined_deg 1.283 r_mcangle_it 1.164 r_mcbond_it 0.699 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.638 r_dihedral_angle_4_deg 19.169 r_dihedral_angle_3_deg 16.687 r_dihedral_angle_1_deg 5.85 r_scangle_it 2.473 r_scbond_it 1.59 r_angle_refined_deg 1.283 r_mcangle_it 1.164 r_mcbond_it 0.699 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.246 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.088 r_metal_ion_refined 0.04 r_bond_refined_d 0.009 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 2604 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 152
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling