2H7X

Pikromycin Thioesterase adduct with reduced triketide affinity label


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MNAPDB ENTRY 1MNA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62961.4 M Li2SO4, 100 mM HEPES 7.6, 80 mM MgCl2, 2 mM DTT, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
3.1661.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.898α = 90
b = 130.728β = 90
c = 56.484γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97922APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.8550990.06724.97.16883368102
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.9292.60.5243.36.1

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MNA1.8583.336883364709333398.610.196120.194190.23219RANDOM36.577
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]
-1.72-0.762.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.909
r_dihedral_angle_3_deg14.576
r_dihedral_angle_4_deg13.858
r_dihedral_angle_1_deg5.018
r_scangle_it3.322
r_mcangle_it3.245
r_scbond_it2.187
r_mcbond_it2.156
r_angle_refined_deg1.235
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.909
r_dihedral_angle_3_deg14.576
r_dihedral_angle_4_deg13.858
r_dihedral_angle_1_deg5.018
r_scangle_it3.322
r_mcangle_it3.245
r_scbond_it2.187
r_mcbond_it2.156
r_angle_refined_deg1.235
r_nbtor_refined0.305
r_nbd_refined0.199
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.12
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4245
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
SCALEPACKdata scaling
MOLREPphasing