4UHH

Structural studies of a thermophilic esterase from Thermogutta terrifontis (cacodylate complex)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
240

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.31α = 90
b = 43.31β = 90
c = 226.85γ = 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
11.0637.8199.70.0618.58.91135602
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)
11.061.0996.20.632.14.8

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 2XUA1.0637.81107919550799.650.103930.102950.12312RANDOM14.171
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]
0.040.020.04-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free31.17
r_dihedral_angle_2_deg30.514
r_dihedral_angle_4_deg15.648
r_dihedral_angle_3_deg12.491
r_sphericity_bonded11.042
r_dihedral_angle_1_deg5.927
r_scbond_it3.958
r_rigid_bond_restr2.785
r_mcangle_it2.223
r_mcbond_it1.705
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free31.17
r_dihedral_angle_2_deg30.514
r_dihedral_angle_4_deg15.648
r_dihedral_angle_3_deg12.491
r_sphericity_bonded11.042
r_dihedral_angle_1_deg5.927
r_scbond_it3.958
r_rigid_bond_restr2.785
r_mcangle_it2.223
r_mcbond_it1.705
r_angle_refined_deg1.699
r_mcbond_other1.651
r_angle_other_deg0.904
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms2104
Nucleic Acid Atoms
Solvent Atoms458
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing