3GUL

T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--ethylbenzene binding


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GUI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527730% PEG 8000, 0.14M magnesium/calcium sulfate, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.141.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.274α = 90
b = 49.274β = 90
c = 129.332γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Si(111)2007-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.000ALS8.2.1

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
12.0746.0599.90.046273.7187392
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)
12.072.1499.90.3313.53.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3GUI2.0746.051773495799.80.23970.236950.29252RANDOM44.25
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]
1.141.14-2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.506
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg16.788
r_dihedral_angle_1_deg5.199
r_scangle_it2.371
r_scbond_it1.499
r_angle_refined_deg1.172
r_mcangle_it0.899
r_mcbond_it0.55
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.506
r_dihedral_angle_4_deg18.681
r_dihedral_angle_3_deg16.788
r_dihedral_angle_1_deg5.199
r_scangle_it2.371
r_scbond_it1.499
r_angle_refined_deg1.172
r_mcangle_it0.899
r_mcbond_it0.55
r_nbtor_refined0.298
r_symmetry_vdw_refined0.254
r_nbd_refined0.2
r_xyhbond_nbd_refined0.16
r_symmetry_hbond_refined0.131
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2586
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms26

Software

Software
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling