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Crystal structure of glycosyltrehalose trehalohydrolase (D252S)
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, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.88 68.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.506 α = 90 b = 78.506 β = 90 c = 282.444 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 MAR CCD 165 mm mirrors 2002-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 2.7 94.15 0.096 18.1 6.1 27427
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 2.7 2.8 89.2 0.193 2.9 3.3
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 2.7 61.5 26037 1384 95.85 0.16177 0.15914 0.1598 0.21188 0.2081 RANDOM 40.901
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] 3.1 1.55 3.1 -4.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_3_deg 21.29 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_1_deg 7.437 r_scangle_it 4.546 r_scbond_it 2.719 r_angle_refined_deg 1.961 r_mcangle_it 1.683 r_mcbond_it 0.846 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.37 r_dihedral_angle_3_deg 21.29 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_1_deg 7.437 r_scangle_it 4.546 r_scbond_it 2.719 r_angle_refined_deg 1.961 r_mcangle_it 1.683 r_mcbond_it 0.846 r_chiral_restr 0.14 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4552 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling