3CW8

4-Chlorobenzoyl-CoA Ligase/Synthetase, bound to 4CBA-Adenylate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27716-24% pentaerythritol propoxylate 426, .1 M K+HEPES, 1 mM ATP, 1 mM 4CBA, pH 6.5-6.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1761.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.583α = 90
b = 128.583β = 90
c = 72.318γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 42005-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97944NSLSX4A

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
12.251597.90.05218.45321683054860.5
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)
12.252.388.60.482.31904

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 REPLACEMENTTHROUGHOUT1T5D2.25153216830548160897.90.198950.198950.1960.25764RANDOM59.44
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]
0.320.160.32-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.385
r_dihedral_angle_4_deg20.213
r_dihedral_angle_3_deg15.154
r_dihedral_angle_1_deg6.266
r_scangle_it3.022
r_scbond_it1.937
r_angle_refined_deg1.448
r_mcangle_it1.207
r_mcbond_it0.707
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.385
r_dihedral_angle_4_deg20.213
r_dihedral_angle_3_deg15.154
r_dihedral_angle_1_deg6.266
r_scangle_it3.022
r_scbond_it1.937
r_angle_refined_deg1.448
r_mcangle_it1.207
r_mcbond_it0.707
r_nbtor_refined0.301
r_symmetry_vdw_refined0.216
r_nbd_refined0.203
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.136
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3723
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms48

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling