6YJX

Structure of Hen egg-white lysozyme crystallized with PAS polypeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5T3F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529312.5 % (w/v) PA200 0.1 M NaOAc 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.0841

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.468α = 90
b = 79.468β = 90
c = 37.848γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2017-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.228.1199.80.0370.04126.028.3573839919.699
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.399.80.9110.9730.8532.448.178

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5T3F1.228.1136485191499.810.14720.14570.1754RANDOM16.255
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]
1.261.26-2.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.833
r_dihedral_angle_4_deg16.1
r_dihedral_angle_3_deg11.571
r_dihedral_angle_1_deg6.31
r_rigid_bond_restr3.121
r_angle_refined_deg1.889
r_angle_other_deg1.614
r_chiral_restr0.114
r_bond_refined_d0.012
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.833
r_dihedral_angle_4_deg16.1
r_dihedral_angle_3_deg11.571
r_dihedral_angle_1_deg6.31
r_rigid_bond_restr3.121
r_angle_refined_deg1.889
r_angle_other_deg1.614
r_chiral_restr0.114
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing