1H87

Gadolinium derivative of tetragonal Hen Egg-White Lysozyme at 1.7 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LYTPBD ENTRY 6LYT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5293NACL 0.8 M, SODIUM ACETATE 50 MM, PH4.5, GD-HP-DO3A 100MM, [PROT]=40 MG/ML, 293 K, pH 4.50
Crystal Properties
Matthews coefficientSolvent content
2.0238.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.25α = 90
b = 77.25β = 90
c = 38.66γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2000-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.7217.299.50.0598.112.512876315.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.8196.80.17348.9

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 REPLACEMENTTHROUGHOUTPBD ENTRY 6LYT1.7227.3323249216997.90.180.180.21RANDOM14.8
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]
-1.31-1.312.62
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_angle_deg1.5
c_scangle_it1.23
c_scbond_it0.87
c_improper_angle_d0.83
c_mcangle_it0.3
c_mcbond_it0.17
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.2
c_angle_deg1.5
c_scangle_it1.23
c_scbond_it0.87
c_improper_angle_d0.83
c_mcangle_it0.3
c_mcbond_it0.17
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms62

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
CNSphasing