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Crystal Structure of T. thermophilus methylenetetrahydrofolate dehydrogenase (MTHFD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 800 mM Potassium sodium tartrate, 100 mM HEPES buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.19 70.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.357 α = 90 b = 121.357 β = 90 c = 59.62 γ = 120
Symmetry Space Group P 32 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 PILATUS 2M Toroidal bendable 2018-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4587 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.152 39.42 92.32 0.087 0.999 19.87 8.53 25688 45.8749638437
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.152 2.229 38.23 1.431 0.433 0.85 2.96
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3P2O 2.15201566872 39.4219349912 1.34350028871 25581 1283 92.3501805054 0.214668092329 0.213132527796 0.2178 0.243890427109 0.2478 51.1275158399
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.58021900707 f_angle_d 0.975296055319 f_chiral_restr 0.0531833663331 f_bond_d 0.00785208552131 f_plane_restr 0.00626947034189
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2127 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 48
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX phasing PHENIX refinement