4E3U

Crystal Structure of Hen Egg White Lysozyme Cryoprotected in Proline


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2LYZPDB entry 2LYZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62961.0M sodium chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
238.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.995α = 90
b = 77.995β = 90
c = 37.74γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IV++2011-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
11.519.49999.60.02846.110.81907619076
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5897.60.2410.2413.18.22660

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 2LYZ1.519.4991891997299.040.18640.18490.215717.3662
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]
-0.1693-0.16930.3386
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.32
f_angle_d1.012
f_chiral_restr0.074
f_bond_d0.005
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms981
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms11

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XDSdata reduction