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Deoxypodophyllotoxin Synthase in complex with Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KUN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M Bis-Tris; 20% (w/v) PEG MME 2000; pH 6.5
20 mg per mL protein
Crystal Properties Matthews coefficient Solvent content 2.1 41.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.713 α = 90 b = 66.828 β = 105.85 c = 55.209 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS EIGER2 XE 16M 2020-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.41 40.13 99.8 0.05 0.03 1 12.6 6.5 56104 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.43 1.4 0.88 0.74 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.41 40.16 53244 2775 99.66 0.1879 0.18625 0.1894 0.21961 0.2199 RANDOM 26.267
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] -1.97 -1.3 2.26 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.483 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_1_deg 6.804 r_long_range_B_refined 6.069 r_long_range_B_other 5.997 r_scangle_other 4.801 r_scbond_it 3.356 r_scbond_other 3.354 r_mcangle_it 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.483 r_dihedral_angle_4_deg 19.043 r_dihedral_angle_3_deg 15.068 r_dihedral_angle_1_deg 6.804 r_long_range_B_refined 6.069 r_long_range_B_other 5.997 r_scangle_other 4.801 r_scbond_it 3.356 r_scbond_other 3.354 r_mcangle_it 3.3 r_mcangle_other 3.3 r_mcbond_it 2.338 r_mcbond_other 2.327 r_angle_refined_deg 1.659 r_angle_other_deg 1.436 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 2377 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing