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Tamavidin2, Novel Avidin-like Biotin-Binding Proteins from an Edible Mushroom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SLG PDB ENTRY 1SLG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.4 25% PEG 3350, 0.2M MgCl2, 0.1M Bis-Tris pH 5.5, 0.1M NaCl, 0.025M MES pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.4K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.382 α = 90 b = 80.017 β = 132.32 c = 55.733 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 1.3 50 97.4 0.118 0.118 2 3.9 61099 61099
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 100 0.47 0.47 1 3.7 6217
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 (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 1SLG 1.3 18.71 57683 3072 97.47 0.20136 0.19943 0.1969 0.23758 0.2342 RANDOM 14.472
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] 0.11 -0.05 -0.09 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_4_deg 23.475 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_1_deg 6.155 r_sphericity_free 2.702 r_sphericity_bonded 2.282 r_scangle_it 2.218 r_scbond_it 1.614 r_angle_refined_deg 1.423 r_mcangle_it 1.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.455 r_dihedral_angle_4_deg 23.475 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_1_deg 6.155 r_sphericity_free 2.702 r_sphericity_bonded 2.282 r_scangle_it 2.218 r_scbond_it 1.614 r_angle_refined_deg 1.423 r_mcangle_it 1.301 r_rigid_bond_restr 0.975 r_mcbond_it 0.837 r_nbtor_refined 0.301 r_nbd_refined 0.252 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_metal_ion_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1876 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing