4ZXI

Crystal Structure of holo-AB3403 a four domain nonribosomal peptide synthetase bound to AMP and Glycine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8287.150.75-0.95 M potassium citrate, 0.01-0.025 M glycine, 0.05 M BTP
Crystal Properties
Matthews coefficientSolvent content
3.968.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.1α = 90
b = 116.1β = 90
c = 342.02γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113.15CCDMARMOSAIC 300 mm CCD2015-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

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
12.945.0399.990.0548.821.952900
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)
12.931000.3362.252

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE2.945.030.0152895297199.970.17590.17440.2249Random Selection53.6487
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.63
f_angle_d1.181
f_chiral_restr0.045
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10077
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms91

Software

Software
Software NamePurpose
Blu-Icedata collection
PDB_EXTRACTdata extraction
SCALAdata scaling
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction