6GF0

Lysozyme structure determined from SFX data using a Sheet-on-Sheet chipless chip


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29320 % NaCl, 6 % PEG 6000, 0.1 M sodium acetate pH 3.0
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.1α = 90
b = 79.1β = 90
c = 39.2γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMPCCD2017-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSACLA BEAMLINE BL31.770SACLABL3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.07401000.9860.0910.32837417
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.072.21000.7730.3242.842

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4n5r2.0739.55741738598.080.200340.198620.23483RANDOM31.191
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.088
r_dihedral_angle_4_deg17.255
r_dihedral_angle_3_deg12.615
r_dihedral_angle_1_deg5.239
r_long_range_B_refined3.217
r_long_range_B_other3.215
r_scangle_other1.898
r_mcangle_it1.458
r_mcangle_other1.457
r_scbond_it1.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.088
r_dihedral_angle_4_deg17.255
r_dihedral_angle_3_deg12.615
r_dihedral_angle_1_deg5.239
r_long_range_B_refined3.217
r_long_range_B_other3.215
r_scangle_other1.898
r_mcangle_it1.458
r_mcangle_other1.457
r_scbond_it1.089
r_scbond_other1.088
r_angle_refined_deg0.962
r_mcbond_it0.851
r_mcbond_other0.85
r_angle_other_deg0.791
r_chiral_restr0.053
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms992
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing