5G1F

Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in complex with coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FLGPDB ENTRY 5FLG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.519% PEG400, 0.1 M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.59α = 90
b = 78.36β = 90
c = 166.43γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2015-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
12.2570.8999.80.0618.86.4322792
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)
12.252.3799.70.7625.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5FLG2.2557.1130569164799.740.218950.217050.25175RANDOM58.666
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]
9.36-6.4-2.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.206
r_dihedral_angle_4_deg20.64
r_dihedral_angle_3_deg15.573
r_dihedral_angle_1_deg7.772
r_angle_refined_deg1.329
r_angle_other_deg0.784
r_chiral_restr0.078
r_gen_planes_refined0.014
r_bond_refined_d0.012
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.206
r_dihedral_angle_4_deg20.64
r_dihedral_angle_3_deg15.573
r_dihedral_angle_1_deg7.772
r_angle_refined_deg1.329
r_angle_other_deg0.784
r_chiral_restr0.078
r_gen_planes_refined0.014
r_bond_refined_d0.012
r_gen_planes_other0.006
r_bond_other_d0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3979
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing