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Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with neokestose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANN PDB ENTRY 5ANN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN WAS CRYSTALLIZED FROM 1.3M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1M TRIS-HCL PH 8.5, THEN SOAKED IN 5MM NEOKESTOSE
Crystal Properties Matthews coefficient Solvent content 4.68 73.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.751 α = 90 b = 205.272 β = 90 c = 145.902 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB MIRRORS 2013-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 2.05 118.92 99.9 0.12 10.1 6.7 141191
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 2.05 2.09 99.8 0.6 3.4 6.8
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 5ANN 2.05 118.92 133984 6957 99.75 0.163 0.16195 0.172 0.18312 0.189 RANDOM 32.436
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] 2.15 -3.47 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 17.791 r_dihedral_angle_3_deg 10.56 r_dihedral_angle_1_deg 6.773 r_scangle_it 3.715 r_scbond_it 2.318 r_mcangle_it 1.936 r_angle_refined_deg 1.494 r_mcbond_it 1.289 r_mcbond_other 1.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_dihedral_angle_4_deg 17.791 r_dihedral_angle_3_deg 10.56 r_dihedral_angle_1_deg 6.773 r_scangle_it 3.715 r_scbond_it 2.318 r_mcangle_it 1.936 r_angle_refined_deg 1.494 r_mcbond_it 1.289 r_mcbond_other 1.288 r_angle_other_deg 1.203 r_chiral_restr 0.113 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_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 9588 Nucleic Acid Atoms Solvent Atoms 1316 Heterogen Atoms 842
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing