3R32

Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant E73A complexed with 4-hydroxyphenacyl CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q4SPDB entry 1Q4S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529820% PEG3400, 100 mM MOPS, 200 mM LiCl, 1 mM 4-HYDROXYPHENACYL COA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5565.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.3α = 90
b = 113.3β = 90
c = 62.7γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORSIEMENS HI-STARgoebel mirrors2002-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.8100900.0650.06529.53.93690936909
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.85650.2820.2823.42.21957

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1Q4S1.898.123690936909195989.880.182730.182730.181040.21604RANDOM33.061
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]
-0.62-0.31-0.620.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.553
r_dihedral_angle_3_deg16.992
r_dihedral_angle_4_deg16.495
r_scangle_it7.421
r_dihedral_angle_1_deg6.198
r_scbond_it4.845
r_mcangle_it3.292
r_angle_refined_deg2.143
r_mcbond_it1.973
r_chiral_restr0.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.553
r_dihedral_angle_3_deg16.992
r_dihedral_angle_4_deg16.495
r_scangle_it7.421
r_dihedral_angle_1_deg6.198
r_scbond_it4.845
r_mcangle_it3.292
r_angle_refined_deg2.143
r_mcbond_it1.973
r_chiral_restr0.171
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2135
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms116

Software

Software
Software NamePurpose
FRAMBOdata collection
AMoREphasing
REFMACrefinement
SAINTdata reduction
SAINTdata scaling