3R3D

Crystal structure of Arthrobacter sp. strain SU 4-hydroxybenzoyl CoA thioesterase mutant T77S 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 MOPS, 200 mM LiCl, 1 mM 4-HYDROXYPHENACYL COA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.3663.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.4α = 90
b = 112.4β = 90
c = 60.4γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORSIEMENS HI-STARgoebel mirrors2002-08-08MSINGLE 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
11.753096.80.0660.06625.53.84092540925
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)
11.751.873.50.2870.2872.11.72262

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 1Q4S1.75304092540925217796.770.195380.195380.193530.23085RANDOM24.482
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]
-0.45-0.23-0.450.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.187
r_dihedral_angle_4_deg15.972
r_dihedral_angle_3_deg14.654
r_scangle_it6.587
r_dihedral_angle_1_deg6.404
r_scbond_it4.709
r_mcangle_it3.082
r_mcbond_it2.099
r_angle_refined_deg1.996
r_chiral_restr0.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.187
r_dihedral_angle_4_deg15.972
r_dihedral_angle_3_deg14.654
r_scangle_it6.587
r_dihedral_angle_1_deg6.404
r_scbond_it4.709
r_mcangle_it3.082
r_mcbond_it2.099
r_angle_refined_deg1.996
r_chiral_restr0.168
r_bond_refined_d0.012
r_gen_planes_refined0.009
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 Atoms2134
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms116

Software

Software
Software NamePurpose
FRAMBOdata collection
AMoREphasing
REFMACrefinement
SAINTdata reduction
SAINTdata scaling