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Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A175W7M4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 1-1 ratio protein to reservoir solution
Protein: 25 mM Tris, pH 7.4, 50 mM potassium chloride, 500 uM FAD, and 1 mM TCEP
Reservoir Solution: 0.1 M HEPES, pH 7.5, 0.1 mM potassium chloride, 20 mM magnesium chloride, 22% poly(acrylic acid sodium salt) 5,100
Crystal Properties Matthews coefficient Solvent content 3 58.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.972 α = 90 b = 151.38 β = 90 c = 188.048 γ = 90
Symmetry Space Group P 21 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 2022-06-30 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 3.41 52.04 99.5 0.164 0.177 0.067 0.996 7.7 6.9 46407
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 3.41 3.53 99.7 2.805 3.024 1.122 0.466 7.1
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 3.49 52.04 41089 2181 99.41 0.21759 0.21556 0.2187 0.25564 0.2558 RANDOM 157.458
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] 7.35 -3.86 -3.49
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.568 r_long_range_B_other 17.568 r_dihedral_angle_3_deg 15.56 r_dihedral_angle_2_deg 11.609 r_mcangle_it 10.921 r_mcangle_other 10.921 r_scangle_other 10.875 r_dihedral_angle_1_deg 7.286 r_mcbond_it 6.929 r_mcbond_other 6.929
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.568 r_long_range_B_other 17.568 r_dihedral_angle_3_deg 15.56 r_dihedral_angle_2_deg 11.609 r_mcangle_it 10.921 r_mcangle_other 10.921 r_scangle_other 10.875 r_dihedral_angle_1_deg 7.286 r_mcbond_it 6.929 r_mcbond_other 6.929 r_scbond_it 6.706 r_scbond_other 6.705 r_angle_refined_deg 1.839 r_angle_other_deg 1.382 r_chiral_restr 0.101 r_gen_planes_refined 0.014 r_bond_refined_d 0.01 r_gen_planes_other 0.009 r_bond_other_d 0.008 r_dihedral_angle_4_deg 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19085 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MrBUMP phasing