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Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MOS PDB ENTRY 3MOS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 279 Reservoir mixture of 13.5-15 % PEG 6000 (w/v), 4% PEG 400 (v/v), 2 % glycerol (v/v) , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.756 α = 90 b = 86.017 β = 125.46 c = 72.994 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 315r mirrors 2011-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93939 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.97 30 92.5 0.047 14.23 3.3 312019 305775 -3 10.555
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 1.04 78.2 0.437 2.74
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS FREE R PDB ENTRY 3MOS 0.97 30 305775 305775 6241 92.6 0.0987 0.0952 0.0952 0.1043 0.121 0.1266 RANDOM 15.9484
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 s_angle_d 311 s_zero_chiral_vol 6 s_non_zero_chiral_vol 6 s_approx_iso_adps 0.132 s_anti_bump_dis_restr 0.11 s_rigid_bond_adp_cmpnt 0.022 s_bond_d 0.014 s_similar_dist s_from_restr_planes s_similar_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4752 Nucleic Acid Atoms Solvent Atoms 963 Heterogen Atoms 100
Software Software Software Name Purpose XSCALE data scaling SHELX refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction PHENIX phasing SHELXL refinement