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1-Epi-Cubenol Synthase from Nonomuraea coxensis (NcECS) in complex with pyrophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.1 M Tris; 0.3 M Mg(Formate)2
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.48 α = 90 b = 88.91 β = 90 c = 101.86 γ = 90
Symmetry Space Group P 21 21 21
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 X 16M 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.8 30 97.4 0.083 12 3.8 58525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 95.5 0.648 2.7
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 1.8 30 55542 2923 97.42 0.1488 0.14697 0.1603 0.18267 0.1938 RANDOM 21.568
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] -2.22 1.94 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.358 r_dihedral_angle_4_deg 17.431 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 5.228 r_long_range_B_refined 2.187 r_long_range_B_other 2.186 r_scangle_other 1.409 r_mcangle_it 1.284 r_mcangle_other 1.283 r_angle_other_deg 1.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.358 r_dihedral_angle_4_deg 17.431 r_dihedral_angle_3_deg 12.501 r_dihedral_angle_1_deg 5.228 r_long_range_B_refined 2.187 r_long_range_B_other 2.186 r_scangle_other 1.409 r_mcangle_it 1.284 r_mcangle_other 1.283 r_angle_other_deg 1.269 r_angle_refined_deg 1.171 r_scbond_it 1.099 r_scbond_other 1.098 r_mcbond_it 0.952 r_mcbond_other 0.952 r_rigid_bond_restr 0.551 r_chiral_restr 0.059 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5180 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing