5DWD

Crystal structure of esterase PE8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.05M Calcium chloride dehydrate;0.1M BIS-TRIS pH 6.5;30%(v/v) Polyethylene glycol monomethyl ether 550
Crystal Properties
Matthews coefficientSolvent content
1.9536.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.772α = 90
b = 73.398β = 102.37
c = 66.403γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9785SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6664.8699.122.546.445616

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6664.8643312230498.170.158130.155830.2001RANDOM25.879
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]
0.61-1.040.48-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.525
r_dihedral_angle_4_deg15.857
r_dihedral_angle_3_deg14.533
r_long_range_B_refined7.393
r_long_range_B_other7.393
r_dihedral_angle_1_deg6.771
r_scangle_other5.231
r_scbond_it3.547
r_scbond_other3.544
r_mcangle_other3.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.525
r_dihedral_angle_4_deg15.857
r_dihedral_angle_3_deg14.533
r_long_range_B_refined7.393
r_long_range_B_other7.393
r_dihedral_angle_1_deg6.771
r_scangle_other5.231
r_scbond_it3.547
r_scbond_other3.544
r_mcangle_other3.456
r_mcangle_it3.449
r_mcbond_it2.418
r_mcbond_other2.401
r_angle_refined_deg2.063
r_angle_other_deg1.161
r_chiral_restr0.168
r_bond_refined_d0.02
r_gen_planes_refined0.012
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3231
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing