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Crystal structure of FrazP2 in complex with forazoline C
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 7.5 293 0.085 M Sodium acetate trihydrate (pH 4.6), 25.5 % PEG 4000, 0.17 M Ammonium acetate and 15 % Glycerol
Crystal Properties Matthews coefficient Solvent content 2.45 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.12 α = 90 b = 74.11 β = 98.13 c = 103.19 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 100 PIXEL DECTRIS EIGER X 16M 2024-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9785 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 43.42 96.85 0.999 22.45 6.5 33285
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 0.997
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 2.3 43.42 33285 1753 96.96 0.21812 0.21499 0.2298 0.27612 0.285 RANDOM 47.891
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.559 r_dihedral_angle_2_deg 11.447 r_long_range_B_refined 10.046 r_long_range_B_other 10.045 r_scangle_other 7.846 r_mcangle_it 6.855 r_mcangle_other 6.854 r_dihedral_angle_1_deg 6.662 r_scbond_it 5.244 r_scbond_other 5.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.559 r_dihedral_angle_2_deg 11.447 r_long_range_B_refined 10.046 r_long_range_B_other 10.045 r_scangle_other 7.846 r_mcangle_it 6.855 r_mcangle_other 6.854 r_dihedral_angle_1_deg 6.662 r_scbond_it 5.244 r_scbond_other 5.243 r_mcbond_it 4.849 r_mcbond_other 4.846 r_angle_refined_deg 1.785 r_angle_other_deg 0.598 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5735 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling PHASES phasing