6M9S

Crystal structure of SeMet SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1 M Tris, pH 8.5, 0.1 M magnesium chloride, 15-30% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7655.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.51α = 90
b = 109.46β = 90
c = 365.98γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.0849.0999.850.0870.0920.99916.9510.06914187539.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.2198.80.9120.9770.7542.067.85

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 DIFFRACTIONSADTHROUGHOUT2.0849.09141875746999.850.175060.174330.18889RANDOM46.72
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]
1.11-0.67-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.888
r_dihedral_angle_4_deg18.693
r_dihedral_angle_3_deg13.071
r_long_range_B_refined5.951
r_long_range_B_other5.951
r_dihedral_angle_1_deg5.131
r_scangle_other3.067
r_mcangle_it2.203
r_mcangle_other2.203
r_scbond_it1.908
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.888
r_dihedral_angle_4_deg18.693
r_dihedral_angle_3_deg13.071
r_long_range_B_refined5.951
r_long_range_B_other5.951
r_dihedral_angle_1_deg5.131
r_scangle_other3.067
r_mcangle_it2.203
r_mcangle_other2.203
r_scbond_it1.908
r_scbond_other1.908
r_mcbond_it1.38
r_mcbond_other1.38
r_angle_refined_deg1.199
r_angle_other_deg1.056
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14639
Nucleic Acid Atoms
Solvent Atoms1237
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
HKL2Mapphasing
SHELXphasing