2QVY

4-Chlorobenzoyl-CoA Ligase/Synthetase, I303G mutation, bound to 3,4-Dichlorobenzoate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T5D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.727714-22% pentaerythritol propoxylate 426, 50 mM BTP, 1 mM ATP, 1 mM 3,4-DCB, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.160.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.813α = 90
b = 127.813β = 90
c = 71.421γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 2102005-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.97930CHESSF2

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
12.763099.50.08811.55.217323
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)
12.762.830.5251.8

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 REPLACEMENTTHROUGHOUT1T5D2.76301644087299.870.194550.191360.25651RANDOM57.054
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]
0.470.230.47-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.099
r_dihedral_angle_4_deg20.782
r_dihedral_angle_3_deg20.472
r_dihedral_angle_1_deg7.375
r_scangle_it4.457
r_mcangle_it4.028
r_scbond_it3.003
r_mcbond_it2.649
r_angle_refined_deg1.692
r_symmetry_vdw_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.099
r_dihedral_angle_4_deg20.782
r_dihedral_angle_3_deg20.472
r_dihedral_angle_1_deg7.375
r_scangle_it4.457
r_mcangle_it4.028
r_scbond_it3.003
r_mcbond_it2.649
r_angle_refined_deg1.692
r_symmetry_vdw_refined0.323
r_nbtor_refined0.322
r_nbd_refined0.242
r_symmetry_hbond_refined0.226
r_xyhbond_nbd_refined0.128
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3716
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing