4N5R

Hen egg-white lysozyme phased using free-electron laser data


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch329320 % NaCl, 6 % PEG 6000, 1 M Na acetate pH 3.0, stored in 8% NaCl, 0.1 M sodium acetate buffer, pH 4.0, soaked in storage solution + 100 mM gadoteridol, batch, temperature 293K
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-ray293PIXELCornell-SLAC Pixel Array Detector (CSPAD)2013-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.45SLAC LCLSCXI

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.1401007294

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VDS2.139.557287729438599.990.23220.230980.25632RANDOM32.54
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]
-0.27-0.270.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.663
r_dihedral_angle_4_deg18.229
r_dihedral_angle_3_deg14.043
r_dihedral_angle_1_deg5.711
r_scangle_it2.224
r_scbond_it1.347
r_angle_refined_deg1.285
r_mcangle_it0.862
r_angle_other_deg0.841
r_mcbond_it0.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.663
r_dihedral_angle_4_deg18.229
r_dihedral_angle_3_deg14.043
r_dihedral_angle_1_deg5.711
r_scangle_it2.224
r_scbond_it1.347
r_angle_refined_deg1.285
r_mcangle_it0.862
r_angle_other_deg0.841
r_mcbond_it0.435
r_mcbond_other0.08
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
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 Atoms52
Heterogen Atoms58

Software

Software
Software NamePurpose
DAQdata collection
PHASERphasing
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling