4M6X

Mutant structure of methyltransferase from Streptomyces hygroscopicus complexed with S-adenosyl-L-homocysteine and methylphenylpyruvic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KIB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529316% PEG3350, 0.2M sodium iodine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.009α = 90
b = 90.219β = 90
c = 136.505γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.97NSRRCBL13C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.330100302643026422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.38100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4KIB2.327.9423026430264161699.530.164940.161570.22745RANDOM35.26
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]
1.750.17-1.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.976
r_dihedral_angle_4_deg17.336
r_dihedral_angle_3_deg16.023
r_long_range_B_refined5.962
r_long_range_B_other5.891
r_dihedral_angle_1_deg5.654
r_scangle_other4.095
r_mcangle_it2.882
r_mcangle_other2.881
r_scbond_it2.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.976
r_dihedral_angle_4_deg17.336
r_dihedral_angle_3_deg16.023
r_long_range_B_refined5.962
r_long_range_B_other5.891
r_dihedral_angle_1_deg5.654
r_scangle_other4.095
r_mcangle_it2.882
r_mcangle_other2.881
r_scbond_it2.518
r_scbond_other2.518
r_mcbond_it1.896
r_mcbond_other1.896
r_angle_refined_deg1.415
r_angle_other_deg0.811
r_chiral_restr0.078
r_bond_refined_d0.01
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 Atoms5232
Nucleic Acid Atoms
Solvent Atoms427
Heterogen Atoms109

Software

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