3GUP

T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine 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
2.0740.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.957α = 90
b = 48.957β = 90
c = 129.315γ = 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
11.548.9697.50.047203.7474022
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)
11.51.5599.50.4633.83.6

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 REPLACEMENTTHROUGHOUT3GUI1.548.9644992240397.560.213440.211340.2534RANDOM29.654
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]
1.21.2-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.371
r_dihedral_angle_3_deg14.979
r_dihedral_angle_4_deg13.407
r_dihedral_angle_1_deg5.291
r_scangle_it3.933
r_scbond_it2.64
r_angle_refined_deg1.643
r_mcangle_it1.579
r_mcbond_it1.217
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.371
r_dihedral_angle_3_deg14.979
r_dihedral_angle_4_deg13.407
r_dihedral_angle_1_deg5.291
r_scangle_it3.933
r_scbond_it2.64
r_angle_refined_deg1.643
r_mcangle_it1.579
r_mcbond_it1.217
r_nbtor_refined0.308
r_nbd_refined0.216
r_xyhbond_nbd_refined0.173
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.15
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms253
Heterogen Atoms31

Software

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