☰ Navigation Tabs
Crystal structure of the complex of dimeric goat lactoperoxidase with diethylene glycol at 2.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 280 0.2M Potassium dihydrogen phosphate 20%w/v PEG 3350, PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 280K
Crystal Properties Matthews coefficient Solvent content 2.57 52.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.199 α = 79.93 b = 75.587 β = 77.86 c = 83.808 γ = 72.5
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 278 IMAGE PLATE MARRESEARCH MIRROR 2006-09-20 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) 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 2.94 25 96 4 28536 28536
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 2OJV 2.94 25 27191 25825 1366 94.99 0.24187 0.20069 0.19744 0.2016 0.23171 0.2667 RANDOM 19.774
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] 0.5 1.39 -0.36 -0.33 0.73 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_dihedral_angle_4_deg 16.115 r_dihedral_angle_3_deg 14.614 r_dihedral_angle_1_deg 5.226 r_scangle_it 1.247 r_angle_refined_deg 1.093 r_scbond_it 0.664 r_mcangle_it 0.622 r_symmetry_hbond_refined 0.347 r_mcbond_it 0.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.837 r_dihedral_angle_4_deg 16.115 r_dihedral_angle_3_deg 14.614 r_dihedral_angle_1_deg 5.226 r_scangle_it 1.247 r_angle_refined_deg 1.093 r_scbond_it 0.664 r_mcangle_it 0.622 r_symmetry_hbond_refined 0.347 r_mcbond_it 0.346 r_symmetry_vdw_refined 0.309 r_nbtor_refined 0.302 r_nbd_refined 0.194 r_metal_ion_refined 0.158 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9514 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 340
Software Software Software Name Purpose DENZO data reduction MOLREP phasing REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling