2RBP

2-(n-propylthio)ethanol in complex with T4 lysozyme L99A/M102Q


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.7755.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.307α = 90
b = 60.307β = 90
c = 97.118γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315KOHZU: Double Crystal Si(111)2007-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.115872ALS8.3.1

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
11.46752.21000.07115.68.63567835678
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)
1.4671.5299.90.4667.23519

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 REPLACEMENTTHROUGHOUT1LGU1.46752.23559735597178499.830.1810.1810.180.206RANDOM16.297
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]
0.150.070.15-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.948
r_dihedral_angle_4_deg14.636
r_dihedral_angle_3_deg10.826
r_dihedral_angle_1_deg4.853
r_sphericity_free2.973
r_scangle_it2.356
r_sphericity_bonded2.197
r_scbond_it1.752
r_mcangle_it1.136
r_angle_refined_deg1.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.948
r_dihedral_angle_4_deg14.636
r_dihedral_angle_3_deg10.826
r_dihedral_angle_1_deg4.853
r_sphericity_free2.973
r_scangle_it2.356
r_sphericity_bonded2.197
r_scbond_it1.752
r_mcangle_it1.136
r_angle_refined_deg1.108
r_rigid_bond_restr1.003
r_mcbond_it0.766
r_nbtor_refined0.306
r_nbd_refined0.19
r_symmetry_vdw_refined0.154
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.12
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1338
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACphasing