2O79

T4 lysozyme with C-terminal extension


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SX7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.62770.9 M K2HPO4, 1.1 M NaH2PO4, pH 6.6, 0.25 M NaCl, 49.0 mM oxidized B mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6653.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.117α = 90
b = 60.117β = 90
c = 97.108γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS II1997-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.82098.40.0750.07552.77.5192101921014.76
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)
11.81.86920.2140.21414.57.41760

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1sx71.820189871898796497.910.150130.150130.148450.18173RANDOM11.308
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]
0.170.090.17-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.203
r_dihedral_angle_4_deg14.67
r_dihedral_angle_3_deg10.944
r_dihedral_angle_1_deg4.998
r_scangle_it3.654
r_scbond_it2.48
r_mcangle_it1.321
r_angle_refined_deg1.284
r_mcbond_it1.053
r_angle_other_deg0.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.203
r_dihedral_angle_4_deg14.67
r_dihedral_angle_3_deg10.944
r_dihedral_angle_1_deg4.998
r_scangle_it3.654
r_scbond_it2.48
r_mcangle_it1.321
r_angle_refined_deg1.284
r_mcbond_it1.053
r_angle_other_deg0.804
r_symmetry_vdw_other0.284
r_xyhbond_nbd_refined0.256
r_mcbond_other0.246
r_nbd_refined0.231
r_symmetry_vdw_refined0.191
r_nbd_other0.183
r_nbtor_refined0.178
r_symmetry_hbond_refined0.177
r_nbtor_other0.081
r_chiral_restr0.071
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1282
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing