1O54

Crystal structure of SAM-dependent O-methyltransferase (TM0748) from Thermotoga maritima at 1.65 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I9G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP529340% MPD, 0.1M sodium acetate trihydrate, pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5751.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.253α = 90
b = 74.992β = 90
c = 143.701γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315flat mirror2003-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6535.9395.90.05517.44.7403344033431.78
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.7478.80.4331.92.24754

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1I9G1.6535.9338297203695.70.159180.157680.18762RANDOM27.161
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]
0.671.31-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.186
r_dihedral_angle_3_deg14.127
r_dihedral_angle_4_deg12.53
r_dihedral_angle_1_deg5.544
r_scangle_it4.32
r_scbond_it2.522
r_mcangle_it1.759
r_angle_refined_deg1.409
r_mcbond_it0.959
r_angle_other_deg0.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.186
r_dihedral_angle_3_deg14.127
r_dihedral_angle_4_deg12.53
r_dihedral_angle_1_deg5.544
r_scangle_it4.32
r_scbond_it2.522
r_mcangle_it1.759
r_angle_refined_deg1.409
r_mcbond_it0.959
r_angle_other_deg0.755
r_symmetry_hbond_refined0.26
r_symmetry_vdw_other0.245
r_xyhbond_nbd_refined0.236
r_nbd_refined0.21
r_symmetry_vdw_refined0.2
r_nbd_other0.181
r_chiral_restr0.083
r_nbtor_other0.082
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2090
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms1

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling