☰ Navigation Tabs
Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, AdoMet-bound, Inhibited (T) State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FCX Trimmed Catalytic domain and trimmed regulatory domain used as invidiual search models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293.15 1-1 protein to reservoir solution,
Protein: 50 mg/mL, 50 mM potassium phosphate buffer (KPB), pH 7.4, containing 500 uM AoMet and 250 uM FAD
Reservoir Solution: 0.1 M sodium acetate, pH 4.8, 0.2 M ammonium sulfate, 6% polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.99 58.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.656 α = 90 b = 149.948 β = 90 c = 171.056 γ = 90
Symmetry Space Group P 2 21 21
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 9M 2022-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.83 75.087 99.8 0.126 0.149 0.077 0.987 10.1 6.9 80491
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.83 2.89 1.171 1.383 0.724 0.672 7.2
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 (All) 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 2.83 74.974 80381 3970 99.603 0.188 0.1873 0.1874 0.2027 0.2026 RANDOM 75.216
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] -0.655 1.49 -0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.794 r_lrange_other 15.554 r_lrange_it 15.551 r_dihedral_angle_3_deg 14.838 r_dihedral_angle_6_deg 13.565 r_scangle_it 9.835 r_scangle_other 9.79 r_mcangle_it 7.466 r_mcangle_other 7.465 r_dihedral_angle_1_deg 6.807
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.794 r_lrange_other 15.554 r_lrange_it 15.551 r_dihedral_angle_3_deg 14.838 r_dihedral_angle_6_deg 13.565 r_scangle_it 9.835 r_scangle_other 9.79 r_mcangle_it 7.466 r_mcangle_other 7.465 r_dihedral_angle_1_deg 6.807 r_scbond_it 6.377 r_scbond_other 6.341 r_mcbond_it 4.894 r_mcbond_other 4.892 r_dihedral_angle_other_2_deg 1.724 r_angle_refined_deg 1.633 r_angle_other_deg 1.37 r_symmetry_nbd_refined 0.196 r_nbd_refined 0.187 r_nbtor_refined 0.166 r_symmetry_nbd_other 0.141 r_nbd_other 0.117 r_xyhbond_nbd_refined 0.108 r_ncsr_local_group_6 0.101 r_chiral_restr 0.094 r_ncsr_local_group_3 0.094 r_ncsr_local_group_1 0.093 r_ncsr_local_group_4 0.093 r_symmetry_xyhbond_nbd_refined 0.092 r_ncsr_local_group_5 0.092 r_ncsr_local_group_2 0.091 r_symmetry_nbtor_other 0.065 r_gen_planes_refined 0.011 r_bond_other_d 0.01 r_bond_refined_d 0.009 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17822 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 502
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing