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Crystal structure of catalytic domain of UGGT (UDP-bound form) from Thermomyces dupontii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 Crystallization buffer 24% PEG 3350, 100 MM TRIS-HCL (PH 9.0), Soaking buffer 24% PEG 3350, 100 MM TRIS-HCL (PH 9.0), 2 mM CaCl2, 10 mM UDP
Crystal Properties Matthews coefficient Solvent content 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.41 α = 90 b = 46.85 β = 90 c = 131.99 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 95 CCD ADSC QUANTUM 315r 2016-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.35 50 99.1 0.088 0.998 12.8 7 62275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.43 94.5 0.796 0.75 6.2
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 5H18 1.35 20 59135 3112 99.08 0.17054 0.1686 0.169 0.20759 0.2091 RANDOM 15.615
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] -0.32 0.75 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.604 r_sphericity_free 16.465 r_dihedral_angle_4_deg 15.919 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_1_deg 6.234 r_sphericity_bonded 4.954 r_long_range_B_refined 2.308 r_long_range_B_other 2.232 r_scangle_other 2.056 r_rigid_bond_restr 1.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.604 r_sphericity_free 16.465 r_dihedral_angle_4_deg 15.919 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_1_deg 6.234 r_sphericity_bonded 4.954 r_long_range_B_refined 2.308 r_long_range_B_other 2.232 r_scangle_other 2.056 r_rigid_bond_restr 1.991 r_scbond_it 1.818 r_scbond_other 1.817 r_angle_refined_deg 1.671 r_mcangle_it 1.468 r_mcangle_other 1.467 r_mcbond_it 1.284 r_mcbond_other 1.28 r_angle_other_deg 0.956 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2240 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing