5AO9

The structure of a novel thermophilic esterase from the Planctomycetes species, Thermogutta terrifontis, Est2-native


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EVQPDB ENTRY 1EVQ

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.6453

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.64α = 90
b = 71.07β = 90
c = 75.84γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXELMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.5847.899.90.0713.36.7467782
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)
11.581.6299.90.8727

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 1EVQ1.5847.8344425229099.870.151360.150130.1749RANDOM29.383
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]
0.7-1.280.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.211
r_dihedral_angle_4_deg18.973
r_dihedral_angle_3_deg15.258
r_dihedral_angle_1_deg5.731
r_scbond_it5.398
r_mcangle_it5.087
r_mcbond_it3.778
r_mcbond_other3.765
r_angle_refined_deg1.486
r_angle_other_deg0.989
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.211
r_dihedral_angle_4_deg18.973
r_dihedral_angle_3_deg15.258
r_dihedral_angle_1_deg5.731
r_scbond_it5.398
r_mcangle_it5.087
r_mcbond_it3.778
r_mcbond_other3.765
r_angle_refined_deg1.486
r_angle_other_deg0.989
r_chiral_restr0.097
r_bond_refined_d0.01
r_gen_planes_refined0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2176
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing