2VSQ

Structure of surfactin A synthetase C (SrfA-C), a nonribosomal peptide synthetase termination module


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AMUPDB ENTRIES 1AMU AND 2JGP
experimental modelPDB 2JGPPDB ENTRIES 1AMU AND 2JGP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M MGCL2, 0.05 M HEPES (PH 7.5), 15 % (W/V) PEG 2000
Crystal Properties
Matthews coefficientSolvent content
2.8756.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.106α = 90
b = 106.562β = 97.35
c = 92.401γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-07-14MMAD
21x-rayMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2
2SYNCHROTRONSLS BEAMLINE X06SA0.9794, 0.9792, 0.9717SLSX06SA

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
12.682.5930.0412.92.245564-379.2
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)
12.62.67680.482

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 DIFFRACTIONMADTHROUGHOUTPDB ENTRIES 1AMU AND 2JGP2.682.544479104093.10.2150.2130.272RANDOM59.23
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]
-1.59-0.03-0.532.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.327
r_dihedral_angle_3_deg19.167
r_dihedral_angle_4_deg18.264
r_dihedral_angle_1_deg7.014
r_scangle_it1.408
r_angle_refined_deg1.272
r_scbond_it0.929
r_angle_other_deg0.878
r_mcangle_it0.765
r_mcbond_it0.463
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.327
r_dihedral_angle_3_deg19.167
r_dihedral_angle_4_deg18.264
r_dihedral_angle_1_deg7.014
r_scangle_it1.408
r_angle_refined_deg1.272
r_scbond_it0.929
r_angle_other_deg0.878
r_mcangle_it0.765
r_mcbond_it0.463
r_nbd_refined0.228
r_symmetry_vdw_other0.202
r_nbd_other0.188
r_nbtor_refined0.186
r_symmetry_vdw_refined0.162
r_xyhbond_nbd_refined0.151
r_symmetry_hbond_refined0.134
r_nbtor_other0.089
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms10056
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing