Navigation Tabs Lysozyme structure based on automated real-time serial crystallography data processing using CrystFEL
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8B3L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROFLUIDIC 3.5 295 Just in-time crystallization (JINXED): a lysozyme solution in acetate buffer (pH 3.5) was mixed with crystallization solution on a running conveyor belt using 3D printed micro nozzles. Crystallization solution: N,N',N'',N''',N'''',N'''''-Hexaacetyl chitohexaose in 33 mM acetate buffer, pH3.5, 6.67% (w/v) PEG4000, 2.07 M NaCl, 6.67% DMSO
Crystal Properties Matthews coefficient Solvent content 2.08 40.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.2 α = 90 b = 79.2 β = 90 c = 38 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 295 PIXEL DECTRIS EIGER X 16M 2023-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 JINXED on TapeDrive injection
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.8 79.365 100 0.98 0.117 5.292 373.9 11716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 100 0.446 1.115 0.94 248.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 56 10264 637 93.31 0.18695 0.18466 0.19 0.22215 0.24 RANDOM 34.619
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] -0.26 -0.26 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.44 r_long_range_B_other 9.602 r_long_range_B_refined 9.599 r_scangle_other 8.456 r_dihedral_angle_1_deg 7.007 r_scbond_it 5.882 r_scbond_other 5.874 r_dihedral_angle_2_deg 4.72 r_mcangle_other 4.64 r_mcangle_it 4.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.44 r_long_range_B_other 9.602 r_long_range_B_refined 9.599 r_scangle_other 8.456 r_dihedral_angle_1_deg 7.007 r_scbond_it 5.882 r_scbond_other 5.874 r_dihedral_angle_2_deg 4.72 r_mcangle_other 4.64 r_mcangle_it 4.594 r_mcbond_it 3.779 r_mcbond_other 3.756 r_angle_refined_deg 1.433 r_angle_other_deg 0.491 r_chiral_restr 0.072 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB-REDO refinement CrystFEL data reduction CrystFEL data scaling PHENIX phasing
