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mouse TDH with NAD+ bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YY7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 283 0.2 M Sodium chloride, 0.1 M HEPES, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.15 α = 90 b = 160.13 β = 90 c = 194.3 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 2012-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 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 2.8 123.572 92.7 0.101 0.115 0.052 11 4.2 53532 53532
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 2.8 2.95 88.1 0.587 0.587 0.306 1.3 4 7329
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 2YY7 2.8 36.42 50776 2700 92.39 0.218 0.2156 0.215 0.2644 0.2637 RANDOM 49.791
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] -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_4_deg 15.666 r_dihedral_angle_3_deg 14.96 r_dihedral_angle_1_deg 4.952 r_mcangle_it 2.203 r_mcbond_it 1.219 r_angle_refined_deg 0.971 r_scbond_it 0.932 r_chiral_restr 0.063 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_4_deg 15.666 r_dihedral_angle_3_deg 14.96 r_dihedral_angle_1_deg 4.952 r_mcangle_it 2.203 r_mcbond_it 1.219 r_angle_refined_deg 0.971 r_scbond_it 0.932 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14495 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 282
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing