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Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose and additives
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UFA PDB ENTRY 1UFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 100 mM sodium acetate (pH 5.5), 15% (w/v) PEG 8000, 10% (v/v) PEG 400, 200 mM sodium chloride, 1% (v/v) dioxane and 5% (v/v) glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.674 α = 90 b = 79.02 β = 90 c = 134.088 γ = 90
Symmetry Space Group P 21 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 MARMOSAIC 225 mm CCD 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
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 1.87 68.08 95.4 0.104 24 10.8 59969 24.6
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) 1.87 1.94 84.3 0.481 2.2 4.8 5216
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 PDB ENTRY 1UFA 1.87 68.08 56854 3024 95.42 0.16107 0.15929 0.1571 0.1959 0.1953 RANDOM 25.03
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] 0.74 0.05 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.516 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 15.61 r_dihedral_angle_1_deg 6.087 r_scangle_it 5.982 r_scbond_it 3.879 r_mcangle_it 2.548 r_angle_refined_deg 2.21 r_mcbond_it 1.554 r_chiral_restr 0.232
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.516 r_dihedral_angle_4_deg 18.264 r_dihedral_angle_3_deg 15.61 r_dihedral_angle_1_deg 6.087 r_scangle_it 5.982 r_scbond_it 3.879 r_mcangle_it 2.548 r_angle_refined_deg 2.21 r_mcbond_it 1.554 r_chiral_restr 0.232 r_bond_refined_d 0.031 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4582 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 86
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling