6RKY

STRUCTURE OF ESTER-HYDROLASE EH1AB1 FROM THE METAGENOME OF LAKE ARREO COMPLEXED WITH A DERIVATIVE OF BIPYRIDINE PHOSPHONATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I8F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529120% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2 M NaF
Crystal Properties
Matthews coefficientSolvent content
2.8556.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.766α = 90
b = 201.92β = 112.19
c = 90.637γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6MKB focusing mirrors2019-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.7949.0899.10.2770.1610.9192.73.83713951.388
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.792.9199.30.5720.3270.7521.63.9

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 REPLACEMENTTHROUGHOUT6I8F2.7949.0835315182399.060.240920.239050.27602RANDOM48.362
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]
2-21.6-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.698
r_dihedral_angle_4_deg18.196
r_dihedral_angle_3_deg14.826
r_long_range_B_refined9.923
r_long_range_B_other9.919
r_scangle_other7.299
r_dihedral_angle_1_deg6.533
r_mcangle_other5.863
r_mcangle_it5.862
r_scbond_it4.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.698
r_dihedral_angle_4_deg18.196
r_dihedral_angle_3_deg14.826
r_long_range_B_refined9.923
r_long_range_B_other9.919
r_scangle_other7.299
r_dihedral_angle_1_deg6.533
r_mcangle_other5.863
r_mcangle_it5.862
r_scbond_it4.639
r_scbond_other4.639
r_mcbond_it3.846
r_mcbond_other3.842
r_angle_refined_deg1.476
r_angle_other_deg1.251
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9628
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing