1ZYT

Crystal structure of spin labeled T4 Lysozyme (A82R1)


X-RAY DIFFRACTION - EPR

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C6T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.8293potassium phosphate, sodium phospahte, sodium choloride, sodium azide, oxidized beta-mercaptoehtanol , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6653.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.293α = 90
b = 60.293β = 90
c = 96.079γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2005-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.78099.80.05741.29.3228852284330.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.760.3145.988.72244

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.752.22165221652117099.830.187090.187090.186120.20564RANDOM18.839
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]
0.220.110.22-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.669
r_dihedral_angle_4_deg10.614
r_dihedral_angle_3_deg10.607
r_dihedral_angle_1_deg3.494
r_scangle_it2.547
r_scbond_it1.717
r_angle_refined_deg1.286
r_mcbond_it0.591
r_nbtor_refined0.298
r_symmetry_vdw_refined0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.669
r_dihedral_angle_4_deg10.614
r_dihedral_angle_3_deg10.607
r_dihedral_angle_1_deg3.494
r_scangle_it2.547
r_scbond_it1.717
r_angle_refined_deg1.286
r_mcbond_it0.591
r_nbtor_refined0.298
r_symmetry_vdw_refined0.204
r_nbd_refined0.2
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.116
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1310
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing