4O1F | pdb_00004o1f

Structure of a methyltransferase component in complex with THF involved in O-demethylation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O0Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5277.15100mM Tris pH 7.5, 100mM succinic acid, 15%(v/v) PEG3350, 4mM THF, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.4249.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.19α = 90
b = 118.24β = 90
c = 57.71γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.830.6299.857921
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.847100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4O0Q1.830.615792154968290299.80.2090.2070.220.2450.25RANDOM21.73
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]
-0.040.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.091
r_dihedral_angle_4_deg21.333
r_dihedral_angle_3_deg16.06
r_dihedral_angle_1_deg6.649
r_angle_refined_deg2.226
r_chiral_restr0.221
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_bond_other_d
r_angle_other_deg
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4061
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms64

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
xia2data reduction
xia2data scaling