☰ Navigation Tabs
Crystal structure of the complex of goat lactoperoxidase with phosphate at 2.94 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GJ1 PDB ENTRY 2GJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 0.1M AMMONIUM DIHYDROGEN PHOSPHATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.15
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) 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 2.94 20 96 0.122 4 27189 27189
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 2.94 2.99 95.3 0.253 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GJ1 2.94 20 27180 25814 1366 95.26 0.18441 0.18319 0.18023 0.21871 RANDOM 15.661
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] 0.41 1.11 -0.36 -0.31 0.51 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_3_deg 18.33 r_dihedral_angle_4_deg 16.408 r_dihedral_angle_1_deg 6.262 r_scangle_it 3.008 r_scbond_it 1.662 r_angle_refined_deg 1.485 r_mcangle_it 1.316 r_mcbond_it 0.681 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.049 r_dihedral_angle_3_deg 18.33 r_dihedral_angle_4_deg 16.408 r_dihedral_angle_1_deg 6.262 r_scangle_it 3.008 r_scbond_it 1.662 r_angle_refined_deg 1.485 r_mcangle_it 1.316 r_mcbond_it 0.681 r_nbtor_refined 0.314 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.143 r_metal_ion_refined 0.105 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9508 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 420
Software Software Software Name Purpose REFMAC refinement DENZO data reduction AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing