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Structural basis for zymogen activation and substrate binding of transglutaminase from Streptomyces mobaraense
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IU4 PDB ENTRY 1IU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 30% PEG8000, 50mM NaCl, 1mM EDTA, 1mM beta-mercaptoethanol, 0.01% NaN3, 100mM cacodylic acid, pH5.0 and 2% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.333 α = 90 b = 67.123 β = 90 c = 83.969 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 180 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.9 20 100 0.043 39.2 8.2 29327 -3 27.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.99 99.9 0.238 0.238 8.1 8 3592
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IU4 1.9 19.129 26318 2953 99.99 0.213 0.21319 0.20971 0.2111 0.24394 0.2454 RANDOM 28.615
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] 0.015 0.004 -0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.947 r_dihedral_angle_4_deg 14.94 r_dihedral_angle_3_deg 14.278 r_dihedral_angle_1_deg 5.142 r_scangle_it 2.579 r_scbond_it 1.554 r_angle_refined_deg 1.056 r_mcangle_it 1.017 r_mcbond_it 0.542 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.947 r_dihedral_angle_4_deg 14.94 r_dihedral_angle_3_deg 14.278 r_dihedral_angle_1_deg 5.142 r_scangle_it 2.579 r_scbond_it 1.554 r_angle_refined_deg 1.056 r_mcangle_it 1.017 r_mcbond_it 0.542 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.189 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.098 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2777 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling