3HTD

(Z)-Thiophene-2-carboxaldoxime in complex with T4 lysozyme L99A/M102Q


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LGUPDB ENTRY 1LGU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52772.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7254.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.26α = 90
b = 60.26β = 90
c = 96.94γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296CCDADSC QUANTUM 315r2007-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11589ALS8.3.1

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
11.43099.80.08711.366.66407134071320.734
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)
1.41.4899.70.5762.76.226131

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 DIFFRACTIONREFMACTHROUGHOUTPDB ENTRY 1LGU1.428.7740712407128151000.1680.1680.1670.19RANDOM15.848
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]
0.440.220.44-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_3_deg10.122
r_dihedral_angle_4_deg10.072
r_dihedral_angle_1_deg4.488
r_sphericity_free3.035
r_scangle_it2.386
r_sphericity_bonded2.353
r_scbond_it1.776
r_rigid_bond_restr1.268
r_angle_refined_deg1.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_3_deg10.122
r_dihedral_angle_4_deg10.072
r_dihedral_angle_1_deg4.488
r_sphericity_free3.035
r_scangle_it2.386
r_sphericity_bonded2.353
r_scbond_it1.776
r_rigid_bond_restr1.268
r_angle_refined_deg1.246
r_mcangle_it1.126
r_mcbond_it0.71
r_nbtor_refined0.307
r_nbd_refined0.219
r_xyhbond_nbd_refined0.171
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.153
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1387
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms29

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
REFMACphasing