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Structure of tectonin 2 from Laccaria bicolor in complex with allyl- alpha_4-methyl-mannoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FSB PDB ENTRY 5FSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.3M MAGNESIUM SULFATE 0.1M MES PH 6.5 80% LITHIUM FORMATE WAS USED AS CROPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.35 47.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.007 α = 90 b = 69.007 β = 90 c = 348.953 γ = 120
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 RAYONIX 2015-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.95 38.77 100 0.14 12.6 7.6 24046 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.41 4.8 7.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5FSB 1.95 38.77 22904 1141 99.96 0.14752 0.14566 0.18476 0.1671 RANDOM 7.791
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] -0.04 -0.02 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 23.667 r_dihedral_angle_2_deg 22.258 r_dihedral_angle_3_deg 14.207 r_dihedral_angle_1_deg 5.871 r_angle_refined_deg 1.711 r_angle_other_deg 1.29 r_scbond_it 0.711 r_mcangle_it 0.621 r_mcbond_it 0.37 r_mcbond_other 0.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 23.667 r_dihedral_angle_2_deg 22.258 r_dihedral_angle_3_deg 14.207 r_dihedral_angle_1_deg 5.871 r_angle_refined_deg 1.711 r_angle_other_deg 1.29 r_scbond_it 0.711 r_mcangle_it 0.621 r_mcbond_it 0.37 r_mcbond_other 0.369 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3329 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing