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Crystal structure of the complex of C-lobe of bovine lactoferrin with maltose at 1.5A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKX PDB entry 1NKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 0.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.484 α = 90 b = 49.846 β = 107.07 c = 65.161 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 203 CCD MARRESEARCH MIRROR 2005-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 0.803 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 1.5 20 90.4 0.065 10 60932 60932 17.84
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 1.5 1.53 99.3 0.484 2.2
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1NKX 1.5 20 53616 1104 90.35 0.1961 0.194 0.1934 0.21862 RANDOM 21.556
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] 1.11 -0.51 -0.92 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 16.999 r_dihedral_angle_1_deg 7.422 r_scangle_it 4.868 r_scbond_it 3.556 r_mcangle_it 2.442 r_mcbond_it 2.238 r_angle_refined_deg 1.744 r_angle_other_deg 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.814 r_dihedral_angle_4_deg 17.404 r_dihedral_angle_3_deg 16.999 r_dihedral_angle_1_deg 7.422 r_scangle_it 4.868 r_scbond_it 3.556 r_mcangle_it 2.442 r_mcbond_it 2.238 r_angle_refined_deg 1.744 r_angle_other_deg 0.97 r_mcbond_other 0.535 r_symmetry_vdw_other 0.3 r_nbd_other 0.236 r_nbd_refined 0.232 r_symmetry_hbond_refined 0.213 r_symmetry_vdw_refined 0.206 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.17 r_nbtor_other 0.115 r_chiral_restr 0.11 r_symmetry_metal_ion_refined 0.099 r_metal_ion_refined 0.057 r_xyhbond_nbd_other 0.015 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing