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Trehalose-6-phosphate from E. coli bound with UDP-glucose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZ5 PDB ENTRY 1GZ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 30% PEG 4000, 200MM AMMONIUM ACETATE, 100MM TRISHCL PH 8
Crystal Properties Matthews coefficient Solvent content 2.4 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.905 α = 90 b = 102.31 β = 90 c = 118.924 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 20 94 0.084 12.4 3.1 69411
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 2.07 68 0.449 1.79 2.2
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 1GZ5 2 19.96 65900 3507 94.2 0.234 0.232 0.2592 0.269 0.2876 RANDOM 21.76
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] -0.31 -0.12 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.179 r_scangle_it 2.787 r_scbond_it 1.841 r_angle_refined_deg 1.49 r_mcangle_it 1.046 r_mcbond_it 0.576 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.22 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.179 r_scangle_it 2.787 r_scbond_it 1.841 r_angle_refined_deg 1.49 r_mcangle_it 1.046 r_mcbond_it 0.576 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.22 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7229 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling AMoRE phasing