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1-Epi-Cubenol Synthase from Nonomuraea coxensis (NcECS): Open State
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 9 277 0.1 M Bicine, 20%; 5 mM MgCl2; 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 3.21 61.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.46 α = 90 b = 133.46 β = 90 c = 93.91 γ = 120
Symmetry Space Group P 6 2 2
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 99.5 0.055 15 5.5 45866
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 1.8 1.9 0.672 2.2 5.3
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 43563 2293 99.48 0.15894 0.15754 0.171 0.18533 0.2013 RANDOM 35.943
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] 0.27 0.13 0.27 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.441 r_dihedral_angle_4_deg 19.088 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_1_deg 4.607 r_long_range_B_refined 2.985 r_long_range_B_other 2.807 r_scangle_other 2.037 r_mcangle_it 1.865 r_mcangle_other 1.865 r_scbond_it 1.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.441 r_dihedral_angle_4_deg 19.088 r_dihedral_angle_3_deg 13.469 r_dihedral_angle_1_deg 4.607 r_long_range_B_refined 2.985 r_long_range_B_other 2.807 r_scangle_other 2.037 r_mcangle_it 1.865 r_mcangle_other 1.865 r_scbond_it 1.592 r_scbond_other 1.592 r_mcbond_it 1.386 r_mcbond_other 1.384 r_angle_other_deg 1.335 r_angle_refined_deg 1.238 r_rigid_bond_restr 0.615 r_chiral_restr 0.066 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 2547 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing