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Cycloalternan-degrading enzyme from Trueperella pyogenes in complex with cycloalternan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution: 5.3 mg/ml, 0.25 M NaCl, 0.01 M Tris-HCl pH 8.3
Crystallization condition: JCSG+ (Qiagen) G7: 0.1 M Succinic acid (pH 7.0) and 15% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.368 α = 90 b = 103.9 β = 90.32 c = 44.798 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 MARMOSAIC 300 mm CCD 2015-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.15 30 99.4 0.094 10.9 3.8 48835
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 2.15 2.19 97.5 0.528 1.9 3.4
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 5F7S 2.15 28.48 46069 2526 99.36 0.1737 0.1717 0.1779 0.21046 0.2182 RANDOM 30.656
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] 1.05 -0.53 -1.07 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.599 r_dihedral_angle_4_deg 18.093 r_dihedral_angle_3_deg 12.951 r_dihedral_angle_1_deg 6.386 r_long_range_B_refined 3.346 r_long_range_B_other 3.346 r_angle_refined_deg 1.377 r_scangle_other 1.36 r_mcangle_it 0.982 r_mcangle_other 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.599 r_dihedral_angle_4_deg 18.093 r_dihedral_angle_3_deg 12.951 r_dihedral_angle_1_deg 6.386 r_long_range_B_refined 3.346 r_long_range_B_other 3.346 r_angle_refined_deg 1.377 r_scangle_other 1.36 r_mcangle_it 0.982 r_mcangle_other 0.982 r_angle_other_deg 0.94 r_scbond_it 0.813 r_scbond_other 0.81 r_mcbond_it 0.588 r_mcbond_other 0.588 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 5789 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing