2RAZ

4-(methylthio)nitrobenzene in complex with T4 lysozyme L99A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 184L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7755.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.322α = 90
b = 60.322β = 90
c = 96.83γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU RAXIS IV2006-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.6452.2799.80.06112.84.62564325592
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)
1.641.799.90.4544.52520

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 REPLACEMENTTHROUGHOUT184L1.64152.272559525546130099.810.1920.1920.1910.221RANDOM15.366
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]
0.130.070.13-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.605
r_dihedral_angle_4_deg16.137
r_dihedral_angle_3_deg11.82
r_dihedral_angle_1_deg4.558
r_scangle_it2.798
r_scbond_it1.881
r_angle_refined_deg1.146
r_mcangle_it1.03
r_mcbond_it0.662
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.605
r_dihedral_angle_4_deg16.137
r_dihedral_angle_3_deg11.82
r_dihedral_angle_1_deg4.558
r_scangle_it2.798
r_scbond_it1.881
r_angle_refined_deg1.146
r_mcangle_it1.03
r_mcbond_it0.662
r_nbtor_refined0.306
r_nbd_refined0.202
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.093
r_chiral_restr0.07
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1322
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing