☰ Navigation Tabs
FPP-Methyltransferase from Pseudomonas chlororaphis in complex with SAH and FPP
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 5.6 293 1.4 M Na/K-Phosphate
Crystal Properties Matthews coefficient Solvent content 2.82 56.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.43 α = 90 b = 100.04 β = 98.03 c = 89.54 γ = 90
Symmetry Space Group C 1 2 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 2024-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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 2.2 30 96.5 0.089 11.1 3.5 111920
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 2.2 2.3 95.3 0.738 2.7 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 30 106293 5594 96.53 0.18595 0.18429 0.21739 0.2085 RANDOM 43.083
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] 0.07 1.52 -0.71 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.395 r_dihedral_angle_4_deg 18.536 r_dihedral_angle_3_deg 13.778 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 3.885 r_long_range_B_other 3.839 r_mcangle_it 2.315 r_mcangle_other 2.315 r_scangle_other 2.165 r_mcbond_it 1.618
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.395 r_dihedral_angle_4_deg 18.536 r_dihedral_angle_3_deg 13.778 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 3.885 r_long_range_B_other 3.839 r_mcangle_it 2.315 r_mcangle_other 2.315 r_scangle_other 2.165 r_mcbond_it 1.618 r_mcbond_other 1.618 r_scbond_it 1.589 r_scbond_other 1.541 r_angle_refined_deg 1.225 r_angle_other_deg 1.091 r_rigid_bond_restr 0.437 r_chiral_restr 0.047 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 14164 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 363
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing