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structure of the complex of C-terminal half (C-lobe) of bovine lactoferrin with alpha-methyl-4-(2-methylpropyl) benzene acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DWA PDB ENTRY 2DWA
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, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.319 α = 90 b = 50.48 β = 107.75 c = 66.116 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 300 IMAGE PLATE MARRESEARCH MIRROR 2007-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.29 20 89 0.125 0.064 15854
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 2.29 2.38 90.2 0.477 1.9
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 PDB ENTRY 2DWA 2.29 20 15841 15027 814 87.3 0.168 0.165 0.1748 0.22 0.2242 RANDOM 32.53
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] -0.02 -0.95 -0.9 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.422 r_dihedral_angle_3_deg 20.348 r_dihedral_angle_4_deg 18.321 r_dihedral_angle_1_deg 7.914 r_scangle_it 5.175 r_scbond_it 3.255 r_mcangle_it 2.191 r_angle_refined_deg 1.71 r_mcbond_it 1.325 r_symmetry_hbond_refined 0.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.422 r_dihedral_angle_3_deg 20.348 r_dihedral_angle_4_deg 18.321 r_dihedral_angle_1_deg 7.914 r_scangle_it 5.175 r_scbond_it 3.255 r_mcangle_it 2.191 r_angle_refined_deg 1.71 r_mcbond_it 1.325 r_symmetry_hbond_refined 0.654 r_symmetry_metal_ion_refined 0.457 r_symmetry_vdw_refined 0.349 r_nbtor_refined 0.314 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.136 r_metal_ion_refined 0.135 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 122
Software Software Software Name Purpose DENZO data reduction AMoRE phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling