4UHF

Structural studies of a thermophilic esterase from Thermogutta terrifontis (L37A mutant with butyrate bound)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XUAPDB ENTRY 2XUA

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0439.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.23α = 90
b = 43.23β = 90
c = 227.83γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.0837.971000.0714.89.31079102
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)
11.081.1199.91.1228.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XUA1.0837.97102497527999.960.114590.113510.13561RANDOM16.721
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]
-0.07-0.04-0.070.24
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.334
r_dihedral_angle_2_deg32.404
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg14.797
r_sphericity_bonded14.058
r_dihedral_angle_1_deg6.247
r_scbond_it5.932
r_mcangle_it3.811
r_mcbond_it2.989
r_mcbond_other2.955
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.334
r_dihedral_angle_2_deg32.404
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg14.797
r_sphericity_bonded14.058
r_dihedral_angle_1_deg6.247
r_scbond_it5.932
r_mcangle_it3.811
r_mcbond_it2.989
r_mcbond_other2.955
r_rigid_bond_restr1.944
r_angle_refined_deg1.806
r_angle_other_deg1.056
r_chiral_restr0.116
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2139
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing