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In-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-MiXD): Aspartate alpha-decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 3.8 293 1:3 protein:mother liquor mixture. 25 mg/mL of ADC in 50 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.1 mM DTT. Mother liquor: 1.95 M (NH4)2SO4, 100 mM citrate/di-sodium phosphate buffer pH 3.8
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.8 α = 90 b = 72.8 β = 90 c = 219 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS EIGER X 4M 2018-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9686 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Split (All) 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 63.05 100 0.04 19.3 6006 24287 30.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.08 100 0.4 4356
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1AW8 2 63.05 22918 1277 99.97 0.15357 0.15183 0.18432 0.1785 RANDOM 36.161
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] 0.11 0.06 0.11 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.595 r_dihedral_angle_1_deg 15.834 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_4_deg 12.093 r_long_range_B_refined 9.465 r_long_range_B_other 9.431 r_scangle_other 7.591 r_scbond_it 4.986 r_scbond_other 4.984 r_mcangle_other 4.937
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.595 r_dihedral_angle_1_deg 15.834 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_4_deg 12.093 r_long_range_B_refined 9.465 r_long_range_B_other 9.431 r_scangle_other 7.591 r_scbond_it 4.986 r_scbond_other 4.984 r_mcangle_other 4.937 r_mcangle_it 4.935 r_mcbond_it 3.637 r_mcbond_other 3.633 r_angle_refined_deg 1.777 r_angle_other_deg 1.341 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1861 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing