2QVZ

4-Chlorobenzoyl-CoA Ligase/Synthetase, I303A mutation, bound to 3-Chlorobenzoate


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, 1mM ATP, 1mM 3-CB, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.160.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.85α = 90
b = 127.85β = 90
c = 71.352γ = 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
12.53092.80.04818.42.222225
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)
12.52.560.322.2

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 REPLACEMENTTHROUGHOUT1T5D2.53022225117799.350.196930.19340.26611RANDOM61.219
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]
0.080.040.08-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.097
r_dihedral_angle_4_deg21.582
r_dihedral_angle_3_deg17.013
r_dihedral_angle_1_deg6.499
r_scangle_it3.654
r_mcangle_it3.357
r_scbond_it2.637
r_mcbond_it2.231
r_angle_refined_deg1.376
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.097
r_dihedral_angle_4_deg21.582
r_dihedral_angle_3_deg17.013
r_dihedral_angle_1_deg6.499
r_scangle_it3.654
r_mcangle_it3.357
r_scbond_it2.637
r_mcbond_it2.231
r_angle_refined_deg1.376
r_nbtor_refined0.306
r_symmetry_vdw_refined0.268
r_nbd_refined0.211
r_symmetry_hbond_refined0.193
r_xyhbond_nbd_refined0.159
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3723
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms10

Software

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