5XUM

Crystal structure of Thermotoga maritima holo-[acyl-carrier-protein] synthase (AcpS)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION827710mM Tris-HCl pH 8.0, 100mM NaCl, 10mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.3563.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.96α = 90
b = 72.96β = 90
c = 84.22γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U11.0000SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.163.18598.20.080.038115.41464537.39
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2198.80.5850.2723.15.5

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 REPLACEMENTTHROUGHOUT1F802.163.181390573998.060.171670.169150.22136RANDOM52.678
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]
-0.09-0.05-0.090.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.649
r_sphericity_free27.582
r_sphericity_bonded18.603
r_dihedral_angle_3_deg13.827
r_dihedral_angle_4_deg9.337
r_dihedral_angle_1_deg5.061
r_rigid_bond_restr3.494
r_angle_refined_deg0.874
r_chiral_restr0.06
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.649
r_sphericity_free27.582
r_sphericity_bonded18.603
r_dihedral_angle_3_deg13.827
r_dihedral_angle_4_deg9.337
r_dihedral_angle_1_deg5.061
r_rigid_bond_restr3.494
r_angle_refined_deg0.874
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1354
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing