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mouse TDH mutant R180K with NAD+ bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris, 20%(w/v) Polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.24 α = 90 b = 154.05 β = 90 c = 199.19 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 CCD ADSC QUANTUM 315r 2014-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97911 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 3.25 121.859 97.4 0.134 0.153 0.073 8.6 4 35778 35778
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.43 94.3 0.566 0.566 0.325 1.3 3.5 4952
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 4YR9 3.25 47.12 33952 1772 96.97 0.2305 0.2276 0.2257 0.2851 0.2815 RANDOM 76.453
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.197 r_dihedral_angle_3_deg 16.004 r_dihedral_angle_4_deg 13.409 r_dihedral_angle_1_deg 5.852 r_mcangle_it 4.631 r_mcbond_it 2.724 r_mcbond_other 2.723 r_angle_refined_deg 1.06 r_angle_other_deg 0.716 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.197 r_dihedral_angle_3_deg 16.004 r_dihedral_angle_4_deg 13.409 r_dihedral_angle_1_deg 5.852 r_mcangle_it 4.631 r_mcbond_it 2.724 r_mcbond_other 2.723 r_angle_refined_deg 1.06 r_angle_other_deg 0.716 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10592 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 264
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing