4M6Y

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
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.16α = 90
b = 89.626β = 90
c = 136.622γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.53099.9240972409722
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.59100

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 REPLACEMENTTHROUGHOUT4KIB2.529.3422409724097129099.090.182160.178310.25476RANDOM52.145
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]
1.672.32-3.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.793
r_dihedral_angle_4_deg18.275
r_dihedral_angle_3_deg16.447
r_long_range_B_refined7.749
r_long_range_B_other7.708
r_dihedral_angle_1_deg6.008
r_scangle_other4.971
r_mcangle_it4.376
r_mcangle_other4.376
r_scbond_it3.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.793
r_dihedral_angle_4_deg18.275
r_dihedral_angle_3_deg16.447
r_long_range_B_refined7.749
r_long_range_B_other7.708
r_dihedral_angle_1_deg6.008
r_scangle_other4.971
r_mcangle_it4.376
r_mcangle_other4.376
r_scbond_it3.031
r_scbond_other3.029
r_mcbond_it2.834
r_mcbond_other2.833
r_angle_refined_deg1.38
r_angle_other_deg0.786
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5246
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms112

Software

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