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4-allyl syringol oxidase from Streptomyces cavernae: complex with Vanillyl alcohol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.06 M of MgCl2 6 H2O, CaCl2 2 H2O, 0.1 M Tris, bicine, 20% glycerol, 10% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.419 α = 90 b = 83.419 β = 90 c = 298.892 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 EIGER R 4M 2022-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.965460 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 74.72 99.1 0.107 0.118 0.048 0.995 8.4 5.4 116790
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 98.9 1.371 1.524 0.636 0.307 4.7
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 1.75 72.24 110831 5790 99 0.196 0.194 0.2013 0.227 0.23 RANDOM 29.61
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] 0.37 0.18 0.37 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.554 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 7.218 r_long_range_B_refined 7.014 r_long_range_B_other 7.002 r_scangle_other 5.065 r_scbond_it 3.374 r_scbond_other 3.374 r_mcangle_other 3.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.554 r_dihedral_angle_4_deg 18.719 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 7.218 r_long_range_B_refined 7.014 r_long_range_B_other 7.002 r_scangle_other 5.065 r_scbond_it 3.374 r_scbond_other 3.374 r_mcangle_other 3.188 r_mcangle_it 3.187 r_mcbond_it 2.369 r_mcbond_other 2.365 r_angle_refined_deg 1.577 r_angle_other_deg 1.389 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 8138 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing