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The GH127, Beta-arabinofuranosidase, BT3674
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris buffer, 0.2M LiSO4, 40% PEG400
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.821 α = 90 b = 136.821 β = 90 c = 135.582 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 PIXEL DECTRIS PILATUS3 6M 2016-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.16 68.4 100 12.9 11.5 77030
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.22 99.9 0.578 1.4 11.6
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 3WKX 2.16 19.75 74000 3944 99.8 0.17844 0.17614 0.1883 0.22072 0.2273 RANDOM 34.617
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_4_deg 16.705 r_dihedral_angle_3_deg 15.332 r_long_range_B_other 9.585 r_long_range_B_refined 9.584 r_dihedral_angle_1_deg 7.378 r_scangle_other 4.762 r_mcangle_it 3.725 r_mcangle_other 3.724 r_scbond_it 3.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_4_deg 16.705 r_dihedral_angle_3_deg 15.332 r_long_range_B_other 9.585 r_long_range_B_refined 9.584 r_dihedral_angle_1_deg 7.378 r_scangle_other 4.762 r_mcangle_it 3.725 r_mcangle_other 3.724 r_scbond_it 3.317 r_scbond_other 3.316 r_mcbond_it 2.789 r_mcbond_other 2.782 r_angle_refined_deg 1.912 r_angle_other_deg 1.1 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9787 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement xia2 data reduction pointless data scaling PHASER phasing