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crystal structure of the complex of bovine lactoferrin C-lobe with Ribose at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.01M znso4, 25% PEG, Monomethyl ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.906 α = 90 b = 49.631 β = 105.88 c = 64.705 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 273 CCD MAR CCD 165 mm MIRROR 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.8088 EMBL/DESY, HAMBURG X31
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 50 99.5 5 2.1 12828 12819 51.2
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 2.54 92 15.8 13.4
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 1NKX 2.5 19.96 12819 12789 655 99.6 0.204 0.204 0.2097 0.228 0.2327 RANDOM 43
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] 17 -12.89 -12.14 -4.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_scangle_it 2.39 c_angle_deg 1.9 c_mcangle_it 1.87 c_improper_angle_d 1.5 c_scbond_it 1.5 c_mcbond_it 1.07 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.8 c_scangle_it 2.39 c_angle_deg 1.9 c_mcangle_it 1.87 c_improper_angle_d 1.5 c_scbond_it 1.5 c_mcbond_it 1.07 c_bond_d 0.011 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2605 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 149
Software Software Software Name Purpose CNS refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing