3EGE

Crystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.227731.0% ethylene glycol, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.8267.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.609α = 90
b = 76.609β = 90
c = 134.815γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97915SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.429.76199.80.1090.1096.0228.71849448.467
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4698.70.7140.7141.15.61335

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 DIFFRACTIONSADTHROUGHOUT2.429.7611846094699.760.1840.1820.202RANDOM70.806
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]
-1.02-0.51-1.021.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.885
r_dihedral_angle_4_deg16.714
r_dihedral_angle_3_deg11.034
r_scangle_it4.935
r_dihedral_angle_1_deg4.394
r_scbond_it3.653
r_mcangle_it2.255
r_angle_refined_deg1.689
r_mcbond_it1.443
r_angle_other_deg1.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.885
r_dihedral_angle_4_deg16.714
r_dihedral_angle_3_deg11.034
r_scangle_it4.935
r_dihedral_angle_1_deg4.394
r_scbond_it3.653
r_mcangle_it2.255
r_angle_refined_deg1.689
r_mcbond_it1.443
r_angle_other_deg1.422
r_symmetry_vdw_other0.209
r_mcbond_other0.179
r_symmetry_vdw_refined0.173
r_nbd_refined0.17
r_nbtor_refined0.153
r_nbd_other0.152
r_xyhbond_nbd_refined0.127
r_chiral_restr0.096
r_symmetry_hbond_refined0.075
r_nbtor_other0.074
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1990
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing