2XHG

Crystal Structure of the Epimerization Domain from the Initiation Module of Tyrocidine Biosynthesis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M POTASSIUM PHOSPHATE, 20% PEG 8000, (20 % GLYCEROL).
Crystal Properties
Matthews coefficientSolvent content
2.0941.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.71α = 90
b = 74.59β = 90
c = 124.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-11-24MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.547.8499.90.0712.34.2720292
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)
11.51.581000.871.84.1

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 DIFFRACTIONMADTHROUGHOUTNONE1.52570891106199.840.159870.159580.1794RANDOM12.852
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]
0.13-0.250.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.598
r_dihedral_angle_4_deg14.985
r_dihedral_angle_3_deg12.323
r_dihedral_angle_1_deg5.345
r_scangle_it4.515
r_mcangle_it3.206
r_scbond_it2.905
r_mcbond_it2.008
r_angle_refined_deg1.195
r_angle_other_deg0.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.598
r_dihedral_angle_4_deg14.985
r_dihedral_angle_3_deg12.323
r_dihedral_angle_1_deg5.345
r_scangle_it4.515
r_mcangle_it3.206
r_scbond_it2.905
r_mcbond_it2.008
r_angle_refined_deg1.195
r_angle_other_deg0.833
r_mcbond_other0.586
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms3634
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
SHELXphasing