☰ Navigation Tabs
In-flow serial synchrotron crystallography using a 3D-printed microfluidic device (3D-MiXD): Lysozyme
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 3 293 30 mg/mL lysozyme in 100 mM NaAc (pH3.0) rapidly mixed in a 1:1 ratio with precipitant (100 mM NaAc pH 3.0, 20% NaCl, 6% PEG 6000)
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.7 α = 90 b = 79.7 β = 90 c = 38.55 γ = 90
Symmetry Space Group P 43 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 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
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 450000 450000
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 3D-printed microfluidic device 0.83 (µl/min) undefined (µm) crystallization buffer
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 56.36 100 0.06 6.21 625 8876 31.3
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 0.57 1.83 448
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 6H79 2 56.36 8437 404 99.98 0.15984 0.15781 0.1701 0.20117 0.2111 RANDOM 36.959
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] -0.38 -0.38 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.477 r_dihedral_angle_4_deg 24.45 r_dihedral_angle_3_deg 15.726 r_long_range_B_other 7.774 r_long_range_B_refined 7.771 r_dihedral_angle_1_deg 6.827 r_scangle_other 6.373 r_scbond_it 4.179 r_scbond_other 4.175 r_mcangle_other 3.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.477 r_dihedral_angle_4_deg 24.45 r_dihedral_angle_3_deg 15.726 r_long_range_B_other 7.774 r_long_range_B_refined 7.771 r_dihedral_angle_1_deg 6.827 r_scangle_other 6.373 r_scbond_it 4.179 r_scbond_other 4.175 r_mcangle_other 3.663 r_mcangle_it 3.643 r_mcbond_it 2.972 r_mcbond_other 2.952 r_angle_refined_deg 1.584 r_angle_other_deg 1.384 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing