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Crystal Structure of C-lobe of Bovine lactoferrin Complexed with 1,2,5-Pentanetriol at 1.98 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IB0
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 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.925 α = 90 b = 50.215 β = 106.88 c = 65.633 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 77 CCD MARRESEARCH mirror 2011-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.98 62.8 95 0.099 7.3 24870 24870
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 1.98 2.05 99.1 0.264 2
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 3IB0 1.98 62.8 24870 24870 1332 94.98 0.20021 0.20021 0.19795 0.1999 0.24112 0.2434 RANDOM 25.034
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] 2.41 -0.74 -1.66 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_4_deg 18.986 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 5.188 r_scangle_it 4.83 r_scbond_it 3.293 r_mcangle_it 2.619 r_angle_refined_deg 1.723 r_mcbond_it 1.685 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_4_deg 18.986 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 5.188 r_scangle_it 4.83 r_scbond_it 3.293 r_mcangle_it 2.619 r_angle_refined_deg 1.723 r_mcbond_it 1.685 r_chiral_restr 0.154 r_bond_refined_d 0.027 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 90
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling