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Crystal structure of the complex of human lactoferrin N-lobe and lactoferrin-binding domain of pneumococcal surface protein A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H45 PDB entry 1H45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 30% (v/v) PEG 400, 0.2 M Lithium Sulfate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.77 67.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.18 α = 90 b = 130.18 β = 90 c = 80.8 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2006-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 2.91 15 99.9 0.098 7 2.9 33745 33481 1
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) 1 2.91 3 100 0.359 3 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1H45 2.91 15 30285 1615 95.23 0.20541 0.20309 0.2011 0.24906 0.2466 RANDOM 31.893
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] 0.94 0.47 0.94 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.014 r_dihedral_angle_4_deg 19.864 r_dihedral_angle_3_deg 17.282 r_dihedral_angle_1_deg 4.99 r_scangle_it 1.808 r_angle_refined_deg 1.167 r_scbond_it 1.062 r_mcangle_it 0.786 r_mcbond_it 0.461 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.014 r_dihedral_angle_4_deg 19.864 r_dihedral_angle_3_deg 17.282 r_dihedral_angle_1_deg 4.99 r_scangle_it 1.808 r_angle_refined_deg 1.167 r_scbond_it 1.062 r_mcangle_it 0.786 r_mcbond_it 0.461 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.122 r_metal_ion_refined 0.111 r_symmetry_metal_ion_refined 0.096 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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_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 6902 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing