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Serial Macromolecular Crystallography at ALBA Synchrotron Light Source - Lysozyme
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 298 0.1 M sodium acetate pH 3.0, 18 % (w/v) sodium chloride, 6% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.08 40.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79 α = 90 b = 79 β = 90 c = 38.2 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 298 PIXEL DECTRIS PILATUS 6M 2018-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 LCP Injection injection
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 undefined (µl/min) undefined (µm)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 38.2 100 0.996 9.8 679 7498 37.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.17 0.207 0.5 161
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 1VDS 2.1 35.35 6723 741 99.97 0.18359 0.17847 0.1905 0.23225 0.2094 RANDOM 47.711
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] -0.64 -0.64 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 18.747 r_dihedral_angle_3_deg 15.004 r_long_range_B_refined 6.713 r_long_range_B_other 6.711 r_dihedral_angle_1_deg 6.542 r_scangle_other 5.398 r_scbond_it 3.563 r_scbond_other 3.56 r_mcangle_other 3.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.69 r_dihedral_angle_4_deg 18.747 r_dihedral_angle_3_deg 15.004 r_long_range_B_refined 6.713 r_long_range_B_other 6.711 r_dihedral_angle_1_deg 6.542 r_scangle_other 5.398 r_scbond_it 3.563 r_scbond_other 3.56 r_mcangle_other 3.261 r_mcangle_it 3.26 r_mcbond_it 2.482 r_mcbond_other 2.478 r_angle_refined_deg 1.389 r_angle_other_deg 1.142 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 17 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction Aimless data scaling MOLREP phasing