☰ Navigation Tabs
FPP-Methyltransferase from Burkholderia territorii in complex with SAH
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 0.1 M HEPES, 25% PEG 3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 3.23 61.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.63 α = 90 b = 108.63 β = 90 c = 73.29 γ = 90
Symmetry Space Group P 41 21 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 2025-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0597 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.4 30 99 0.066 13.6 5.5 85663
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 1.4 1.5 99.7 0.781 2.3 5.2
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 1.4 30 81328 4280 99.07 0.14651 0.14537 0.1469 0.1683 0.1695 RANDOM 21.905
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.697 r_dihedral_angle_4_deg 15.779 r_dihedral_angle_3_deg 12.909 r_dihedral_angle_1_deg 6.078 r_long_range_B_refined 4.139 r_long_range_B_other 3.651 r_scangle_other 3.041 r_scbond_it 2.703 r_scbond_other 2.373 r_mcangle_it 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.697 r_dihedral_angle_4_deg 15.779 r_dihedral_angle_3_deg 12.909 r_dihedral_angle_1_deg 6.078 r_long_range_B_refined 4.139 r_long_range_B_other 3.651 r_scangle_other 3.041 r_scbond_it 2.703 r_scbond_other 2.373 r_mcangle_it 2.326 r_mcangle_other 2.326 r_mcbond_it 1.759 r_mcbond_other 1.759 r_angle_refined_deg 1.391 r_angle_other_deg 1.386 r_rigid_bond_restr 1.322 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 2208 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing