4TWS

Gadolinium Derivative of Tetragonal Hen Egg-White Lysozyme at 1.45 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H87 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5294Tetragonal crystals were grown by the vapour-diffusion technique using the hanging-drop method, with 0.7-1.0 M sodium chloride and 50 mM sodium acetate buffer at pH 4.5. Derivative crystals containing gadolinium were obtained using concentrations of Gd-HPDO3A in the range 10-100 mM.
Crystal Properties
Matthews coefficientSolvent content
2.0239.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.22α = 90
b = 77.22β = 90
c = 38.81γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 315r2007-06-26MSINGLE WAVELENGTH
21x-ray90CCDADSC QUANTUM 3152007-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.10.979340ALS8.3.1
2SYNCHROTRONALS BEAMLINE 12.3.10.979340ALS12.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.4538.6187.80.04517.573.419784-311.64
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.49390.2821.861.3

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1H871.4538.611978397592.60.1390.1380.16115.7
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d22.416
f_angle_d1.424
f_chiral_restr0.065
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms105

Software

Software
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction