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PglE Aminotransferase in complex with External Aldimine, Mutant K184A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O61 PDB 1O61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 15-18% PEG3350, 1 mM PLP, 10 mM UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose, 100 mM MOPS, 200 mM tetraethylammoniumchloride
Crystal Properties Matthews coefficient Solvent content 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.161 α = 90 b = 66.161 β = 90 c = 169.013 γ = 90
Symmetry Space Group P 41 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 CCD Bruker Platinum 135 2015-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 30 99.9 0.053 0.053 15.1 13.6 26017 26017
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 2.1 97.4 0.237 2.8 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1O61 2 29.61 26017 24687 1330 99.06 0.19184 0.18835 0.193 0.25445 0.2539 RANDOM 25.058
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] 0.36 0.36 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.892 r_dihedral_angle_3_deg 16.662 r_dihedral_angle_4_deg 11.858 r_dihedral_angle_1_deg 6.943 r_angle_refined_deg 1.715 r_angle_other_deg 0.824 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.892 r_dihedral_angle_3_deg 16.662 r_dihedral_angle_4_deg 11.858 r_dihedral_angle_1_deg 6.943 r_angle_refined_deg 1.715 r_angle_other_deg 0.824 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 3075 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing