5DZT

Crystal structure of class II lanthipeptide synthetase CylM in complex with AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2770.2 M CaCl, 0.1 M HEPES, pH 7.5, 10 mM betaine hydrochloride, and 28% PEG 400; 0.2 M KCl, 0.05 M HEPES pH7.5, 10 mM barium chloride, and 33% 5/4 PO/OH
Crystal Properties
Matthews coefficientSolvent content
2.4649.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.191α = 90
b = 90.699β = 90
c = 246.361γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX-3002014-04-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.987APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.22587.427.96.251875

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.22549239263687.420.245420.243850.275RANDOM45.95
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]
0.5-0.13-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.163
r_dihedral_angle_3_deg17.388
r_dihedral_angle_4_deg17.214
r_dihedral_angle_1_deg5.78
r_angle_refined_deg1.308
r_chiral_restr0.092
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.163
r_dihedral_angle_3_deg17.388
r_dihedral_angle_4_deg17.214
r_dihedral_angle_1_deg5.78
r_angle_refined_deg1.308
r_chiral_restr0.092
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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 Atoms7251
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
SHELXDphasing
SHARPphasing
HKL-2000data scaling
HKL-2000data reduction