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Crystal structure of glycosyltrehalose trehalohydrolase (D252S) complexed with maltotriosyltrehalose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 1.1M sodium citrate, 0.1M HEPES, 5mM MTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.87 68.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.441 α = 90 b = 78.441 β = 90 c = 282.277 γ = 120
Symmetry Space Group P 32 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 4r mirrors 2001-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 1.0000 SPring-8 BL40B2
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 2.3 94.09 99.9 0.087 40.5 9.6 45920
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 2.3 2.38 99.3 0.366 4.5 7.1
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 1EH9 2.3 68 45823 2314 99.82 0.1794 0.1774 0.1748 0.2176 0.211 RANDOM 47.1878
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] 2.92 1.46 2.92 -4.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_3_deg 19.687 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_1_deg 6.668 r_scangle_it 3.999 r_scbond_it 2.556 r_angle_refined_deg 1.694 r_mcangle_it 1.521 r_mcbond_it 0.792 r_chiral_restr 0.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.309 r_dihedral_angle_3_deg 19.687 r_dihedral_angle_4_deg 16.75 r_dihedral_angle_1_deg 6.668 r_scangle_it 3.999 r_scbond_it 2.556 r_angle_refined_deg 1.694 r_mcangle_it 1.521 r_mcbond_it 0.792 r_chiral_restr 0.153 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4552 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 83
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling