4UHD

Structural studies of a thermophilic esterase from Thermogutta terrifontis (acetate bound)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0640.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.28α = 90
b = 43.28β = 90
c = 227.29γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXELMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.0737.4890.50.0333.39.1999372
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)
11.071.151.10.285.65.5

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 2XUA1.0737.4895076485690.150.094430.093510.11203RANDOM13.802
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]
0.020.010.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.712
r_dihedral_angle_2_deg28.688
r_dihedral_angle_4_deg16.862
r_dihedral_angle_3_deg13.925
r_sphericity_bonded12.171
r_mcangle_it7.314
r_mcbond_other6.867
r_mcbond_it6.857
r_dihedral_angle_1_deg5.809
r_scbond_it5.706
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free32.712
r_dihedral_angle_2_deg28.688
r_dihedral_angle_4_deg16.862
r_dihedral_angle_3_deg13.925
r_sphericity_bonded12.171
r_mcangle_it7.314
r_mcbond_other6.867
r_mcbond_it6.857
r_dihedral_angle_1_deg5.809
r_scbond_it5.706
r_rigid_bond_restr2.896
r_angle_refined_deg1.836
r_angle_other_deg1.062
r_chiral_restr0.105
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms2108
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing