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Lysozyme structure determined from SFX data using a Sheet-on-Sheet chipless chip
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 20 % NaCl, 6 % PEG 6000, 0.1 M sodium acetate pH 3.0
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.1 α = 90 b = 79.1 β = 90 c = 39.2 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 293 CCD MPCCD 2017-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.770 SACLA BL3
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 2.07 40 100 0.986 0.09 10.3 283 7417
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 2.07 2.2 100 0.773 0.324 2.8 42
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 FOURIER SYNTHESIS THROUGHOUT 4n5r 2.07 39.55 7417 385 98.08 0.20034 0.19862 0.2075 0.23483 0.2782 RANDOM 31.191
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] -0.37 -0.37 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.088 r_dihedral_angle_4_deg 17.255 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 5.239 r_long_range_B_refined 3.217 r_long_range_B_other 3.215 r_scangle_other 1.898 r_mcangle_it 1.458 r_mcangle_other 1.457 r_scbond_it 1.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.088 r_dihedral_angle_4_deg 17.255 r_dihedral_angle_3_deg 12.615 r_dihedral_angle_1_deg 5.239 r_long_range_B_refined 3.217 r_long_range_B_other 3.215 r_scangle_other 1.898 r_mcangle_it 1.458 r_mcangle_other 1.457 r_scbond_it 1.089 r_scbond_other 1.088 r_angle_refined_deg 0.962 r_mcbond_it 0.851 r_mcbond_other 0.85 r_angle_other_deg 0.791 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 992 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling REFMAC phasing