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Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.5 277 Ethanol, Tris-HCL, pH 6.5, MICRODIALYSIS, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.156 α = 90 b = 98.09 β = 90 c = 157.036 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU MIRROR 2003-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5414
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 2.5 20 96.8 0.059 9.9 12.1 367651 30469 53.3
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 2.5 2.56 93 0.602 2.5
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 1B0L 2.5 19.73 30468 28929 1539 100 0.22 0.2044 0.20381 0.21517 RANDOM 48.154
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] 1.61 1.13 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.075 r_scangle_it 3.742 r_dihedral_angle_1_deg 2.304 r_scbond_it 2.19 r_angle_refined_deg 1.728 r_mcangle_it 1.675 r_angle_other_deg 1.125 r_mcbond_it 0.884 r_nbtor_other 0.472 r_nbd_refined 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.075 r_scangle_it 3.742 r_dihedral_angle_1_deg 2.304 r_scbond_it 2.19 r_angle_refined_deg 1.728 r_mcangle_it 1.675 r_angle_other_deg 1.125 r_mcbond_it 0.884 r_nbtor_other 0.472 r_nbd_refined 0.256 r_symmetry_vdw_refined 0.243 r_nbd_other 0.24 r_symmetry_vdw_other 0.228 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_other 0.139 r_chiral_restr 0.118 r_xyhbond_nbd_other 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5347 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing