2RBR

2-phenoxyethanol 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
2.7354.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.135α = 90
b = 60.135β = 90
c = 96.307γ = 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
11.43352.0699.90.07615.85.53745737457
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)
1.4331.481000.3765.23708

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 DIFFRACTIONTHROUGHOUT1LGU1.43352.063741237412187599.40.1810.1810.180.2RANDOM15.595
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]
-0.08-0.04-0.080.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.265
r_dihedral_angle_4_deg16.814
r_dihedral_angle_3_deg11.607
r_dihedral_angle_1_deg4.587
r_sphericity_free2.881
r_scangle_it2.495
r_sphericity_bonded2.059
r_scbond_it1.88
r_angle_refined_deg1.122
r_rigid_bond_restr1.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.265
r_dihedral_angle_4_deg16.814
r_dihedral_angle_3_deg11.607
r_dihedral_angle_1_deg4.587
r_sphericity_free2.881
r_scangle_it2.495
r_sphericity_bonded2.059
r_scbond_it1.88
r_angle_refined_deg1.122
r_rigid_bond_restr1.098
r_mcangle_it1.048
r_mcbond_it0.795
r_nbtor_refined0.307
r_nbd_refined0.199
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.17
r_xyhbond_nbd_refined0.131
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1358
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms15

Software

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