4M74

Mutant structure of methyltransferase from Streptomyces hygroscopicus


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
2.2645.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.391α = 90
b = 89.916β = 90
c = 137.559γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

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
12.23099.9311113111122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.24100

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 REPLACEMENTTHROUGHOUT4KIB2.226.8323111131111163588.150.168420.164940.23408RANDOM35.98
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]
0.180.14-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.26
r_dihedral_angle_3_deg16.874
r_dihedral_angle_4_deg14.269
r_long_range_B_refined8.027
r_long_range_B_other7.915
r_dihedral_angle_1_deg6.082
r_scangle_other5.492
r_mcangle_it4.336
r_mcangle_other4.335
r_scbond_it3.404
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.26
r_dihedral_angle_3_deg16.874
r_dihedral_angle_4_deg14.269
r_long_range_B_refined8.027
r_long_range_B_other7.915
r_dihedral_angle_1_deg6.082
r_scangle_other5.492
r_mcangle_it4.336
r_mcangle_other4.335
r_scbond_it3.404
r_scbond_other3.404
r_mcbond_it2.854
r_mcbond_other2.854
r_angle_refined_deg1.727
r_angle_other_deg0.879
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5216
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms108

Software

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