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Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 with bound 5,10-methylene tetrahydromethanopterin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y5Y Formaldehyde-activating enzyme from Methylobacterium extorquens AM1 PDB ID 1Y5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 281 0.1 M HEPES/NaOH pH 7.5, 20% (w/v) polyethyleneglycol 10,000, 5 mM tetrahydromethanopterin (H4MPT), VAPOR DIFFUSION, HANGING DROP, temperature 281.0K
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.86 α = 90 b = 112.59 β = 91 c = 72.01 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 77 CCD ADSC QUANTUM 4r 2003-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939270 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 1.9 44.82 93.5 0.144 0.082 12.15 3.7 59516 57191 -3 20.9
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) 1 1.9 2.01 76.1 0.5 0.4 3.03 3.2 8288
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 Formaldehyde-activating enzyme from Methylobacterium extorquens AM1 PDB ID 1Y5Y 1.9 44.82 57191 57191 2967 96.9 0.225 0.225 0.209 0.2101 0.241 0.2428 RANDOM 29
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] 18.76 6.46 -9.77 -8.99
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 4.66 c_scbond_it 3.53 c_mcangle_it 2.97 c_mcbond_it 2.32 c_angle_deg 1.6 c_improper_angle_d 1.07 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6293 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 225
Software Software Software Name Purpose DENZO data reduction XDS data reduction EPMR phasing CNS refinement XDS data scaling