3OFJ

Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OFKNodS from NodS-SAH complex (3OFK)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.929228% PEG 3350, 0.1 M magnesium chloride, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.7429.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.7α = 90
b = 48.7β = 90
c = 141.53γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2007-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8086EMBL/DESY, HAMBURGX13

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
12.422099.60.08716.76.746954-359.1
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)
12.422.5197.30.442.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTR-FREENodS from NodS-SAH complex (3OFK)2.4320-353007680.21270.20330.2764RANDOM80.922
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]
-0.17-0.170.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.212
r_dihedral_angle_3_deg18.855
r_dihedral_angle_4_deg18.501
r_scangle_it7.843
r_dihedral_angle_1_deg6.905
r_scbond_it5.171
r_mcangle_it1.934
r_angle_refined_deg1.843
r_mcbond_it0.955
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.212
r_dihedral_angle_3_deg18.855
r_dihedral_angle_4_deg18.501
r_scangle_it7.843
r_dihedral_angle_1_deg6.905
r_scbond_it5.171
r_mcangle_it1.934
r_angle_refined_deg1.843
r_mcbond_it0.955
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.006
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1326
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling