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Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FTR PDB ID 1FTR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 12-18 % PEG 8000, 20 % glycerol, 0.5 M KCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85 α = 90 b = 74.15 β = 113.54 c = 103.87 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 200 CCD ADSC QUANTUM 4 2004-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.91 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2 104 94.7 0.126 0.105 7.93 3 77164 75995 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.1 91.7 0.502 0.413 3.38 2.85 9923
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ID 1FTR 2 20 75995 75995 3870 96.4 0.221 0.221 0.219 0.2285 0.256 0.2221 RANDOM 29.712
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] 4.91 1.84 -2.9 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.876 r_dihedral_angle_4_deg 17.427 r_dihedral_angle_3_deg 15.148 r_dihedral_angle_1_deg 8.311 r_scangle_it 5.223 r_scbond_it 3.454 r_mcangle_it 1.856 r_angle_other_deg 1.77 r_angle_refined_deg 1.613 r_mcbond_it 1.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.876 r_dihedral_angle_4_deg 17.427 r_dihedral_angle_3_deg 15.148 r_dihedral_angle_1_deg 8.311 r_scangle_it 5.223 r_scbond_it 3.454 r_mcangle_it 1.856 r_angle_other_deg 1.77 r_angle_refined_deg 1.613 r_mcbond_it 1.136 r_mcbond_other 0.371 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.243 r_symmetry_vdw_other 0.24 r_xyhbond_nbd_refined 0.206 r_symmetry_hbond_refined 0.201 r_nbd_other 0.193 r_nbtor_refined 0.191 r_metal_ion_refined 0.181 r_nbtor_other 0.091 r_chiral_restr 0.072 r_xyhbond_nbd_other 0.022 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8950 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 417
Software Software Software Name Purpose DENZO data reduction XSCALE data scaling EPMR phasing REFMAC refinement