4UHC

Structural studies of a thermophilic esterase from Thermogutta terrifontis (Native)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0238.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.19α = 90
b = 43.19β = 90
c = 226.63γ = 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 I03DiamondI03

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
11.0375.598.40.0618.581210702
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)
11.031.06840.622.42.9

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 2XUA1.0375.54115070599898.340.110.109040.12853RANDOM14.386
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]
0.10.050.1-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.25
r_dihedral_angle_2_deg31.453
r_dihedral_angle_4_deg18.139
r_dihedral_angle_3_deg14.255
r_sphericity_bonded11.002
r_dihedral_angle_1_deg5.858
r_scbond_it3.594
r_rigid_bond_restr2.121
r_mcangle_it1.979
r_angle_refined_deg1.572
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.25
r_dihedral_angle_2_deg31.453
r_dihedral_angle_4_deg18.139
r_dihedral_angle_3_deg14.255
r_sphericity_bonded11.002
r_dihedral_angle_1_deg5.858
r_scbond_it3.594
r_rigid_bond_restr2.121
r_mcangle_it1.979
r_angle_refined_deg1.572
r_mcbond_it1.436
r_mcbond_other1.435
r_angle_other_deg0.87
r_chiral_restr0.095
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.002
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 Atoms2142
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing