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Human MTHFD2 in complex with DS44960156
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 28% i-PrOH, 0.1M bis-Tris, pH 6.5, 3% PEG 200, 10 mM spermidine
Crystal Properties Matthews coefficient Solvent content 3.14 60.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.424 α = 90 b = 116.424 β = 90 c = 113.178 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 2.25 46.05 100 0.098 0.104 0.032 0.986 13.8 8.6 41331
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 2.25 2.31 99.6 0.937 1.08 0.529 0.574 4.2
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 1DIA 2.25 25 39113 2147 99.88 0.2031 0.2009 0.2012 0.2432 0.2428 RANDOM 50.704
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] 1.44 0.72 1.44 -4.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.286 r_dihedral_angle_4_deg 21.245 r_dihedral_angle_3_deg 18.002 r_dihedral_angle_1_deg 6.842 r_angle_refined_deg 1.626 r_chiral_restr 0.105 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4375 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 144
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing