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Crystal structure of human mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase (MTHFD2) in complex with LY345899 and cofactors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Phosphate/Citrate pH 4.1, 38 % v/v PEG300, in presence of 1:50 ratio each of trypsin, alpha-chymotrypsin, pepsin, papain, proteinase K and subtilisin to MTHFD2
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.323 α = 90 b = 74.323 β = 90 c = 98.62 γ = 90
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 2015-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.89 37.16 99.8 0.316 0.98 6.8 6.9 21322
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.93 96.8 4.348 0.297 0.9 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1B0A 1.89 37.16 20245 1073 99.76 0.16509 0.1626 0.1738 0.21222 0.2206 RANDOM 28.27
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.827 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 15.236 r_long_range_B_refined 6.253 r_long_range_B_other 6.066 r_dihedral_angle_1_deg 6.042 r_scangle_other 2.602 r_angle_refined_deg 2.276 r_scbond_it 1.642 r_scbond_other 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.827 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 15.236 r_long_range_B_refined 6.253 r_long_range_B_other 6.066 r_dihedral_angle_1_deg 6.042 r_scangle_other 2.602 r_angle_refined_deg 2.276 r_scbond_it 1.642 r_scbond_other 1.64 r_mcangle_other 1.431 r_mcangle_it 1.43 r_angle_other_deg 1.17 r_mcbond_it 0.901 r_mcbond_other 0.897 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2216 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing