4M71

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
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.833α = 90
b = 93.693β = 90
c = 137.375γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A1.0NSRRCBL15A

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
12.23099.9346113461122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.28100

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 REPLACEMENTTHROUGHOUT4KIB2.2128.9523461134611183590.290.161960.158420.22872RANDOM31.392
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]
0.46-0.29-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_4_deg18.09
r_dihedral_angle_3_deg16.876
r_long_range_B_refined7.592
r_long_range_B_other7.488
r_dihedral_angle_1_deg6.607
r_scangle_other5.081
r_mcangle_it3.622
r_mcangle_other3.619
r_scbond_it3.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_4_deg18.09
r_dihedral_angle_3_deg16.876
r_long_range_B_refined7.592
r_long_range_B_other7.488
r_dihedral_angle_1_deg6.607
r_scangle_other5.081
r_mcangle_it3.622
r_mcangle_other3.619
r_scbond_it3.21
r_scbond_other3.209
r_mcbond_it2.349
r_mcbond_other2.348
r_angle_refined_deg1.775
r_angle_other_deg0.891
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5173
Nucleic Acid Atoms
Solvent Atoms529
Heterogen Atoms119

Software

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