2HUK

Crystal structure of T4 Lysozyme V131C synthetic dimer


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1C6TPDB entry 1C6T

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529520% PEG 8000, 0.1M Na Cacodylate, pH 6.5, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.2745.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.267α = 90
b = 29.408β = 97.39
c = 31.243γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2004-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
11.82596.80.06814.3152872
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)
1.81.8693.50.4452.05

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1C6T2252112991073056797.80.1810.1780.24RANDOM14.05
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]
0.630.27-1.030.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.557
r_dihedral_angle_4_deg18.283
r_dihedral_angle_3_deg15.324
r_dihedral_angle_1_deg5.937
r_scangle_it5.015
r_scbond_it3.437
r_mcangle_it1.754
r_angle_refined_deg1.715
r_mcbond_it1.216
r_symmetry_vdw_refined0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.557
r_dihedral_angle_4_deg18.283
r_dihedral_angle_3_deg15.324
r_dihedral_angle_1_deg5.937
r_scangle_it5.015
r_scbond_it3.437
r_mcangle_it1.754
r_angle_refined_deg1.715
r_mcbond_it1.216
r_symmetry_vdw_refined0.36
r_nbtor_refined0.297
r_nbd_refined0.226
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.158
r_chiral_restr0.127
r_bond_refined_d0.022
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1316
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing