3G5L

Crystal structure of putative S-adenosylmethionine dependent methyltransferase from Listeria monocytogenes


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52941M Lithium chloride pH 7.5, 100mM Sodium acetate, 30% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.2344.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.812α = 90
b = 92.532β = 90
c = 99.973γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMAR CCD 165 mm2008-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
12.355090.70.1215.66.322700-0.5
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)
2.352.4399.80.432.75.6

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 DIFFRACTIONSADTHROUGHOUT2.35201987367090.70.192350.189530.27618RANDOM30.473
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]
1.850.79-2.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.831
r_dihedral_angle_3_deg17.88
r_scangle_it15.198
r_dihedral_angle_4_deg14.483
r_scbond_it12.288
r_mcangle_it7.886
r_mcbond_it6.082
r_dihedral_angle_1_deg6
r_angle_refined_deg1.199
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.831
r_dihedral_angle_3_deg17.88
r_scangle_it15.198
r_dihedral_angle_4_deg14.483
r_scbond_it12.288
r_mcangle_it7.886
r_mcbond_it6.082
r_dihedral_angle_1_deg6
r_angle_refined_deg1.199
r_nbtor_refined0.295
r_xyhbond_nbd_refined0.162
r_nbd_refined0.139
r_symmetry_hbond_refined0.122
r_symmetry_vdw_refined0.111
r_chiral_restr0.086
r_bond_refined_d0.008
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 Atoms3639
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms2

Software

Software
Software NamePurpose
MAR345data collection
SHELXDphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling