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Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with adenosine at 2.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES, PEG, MONOMETHYLETHER, 0.1M ZNSO4 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.317 α = 90 b = 50.465 β = 107.66 c = 65.919 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 291 IMAGE PLATE MAR scanner 345 mm plate 2006-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.4 63.25 97.6 15352 15352
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 2.4 2.43 99.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2B6D 2.4 20 15352 14577 767 97.42 0.2 0.19387 0.19238 0.22267 RANDOM 29.55
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] -0.29 -1.26 -0.18 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.277 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.748 r_scbond_it 2.168 r_angle_refined_deg 1.945 r_mcangle_it 1.561 r_mcbond_it 0.825 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.234 r_symmetry_hbond_refined 0.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.277 r_dihedral_angle_1_deg 5.284 r_scangle_it 3.748 r_scbond_it 2.168 r_angle_refined_deg 1.945 r_mcangle_it 1.561 r_mcbond_it 0.825 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.234 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.125 r_metal_ion_refined 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2605 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing