3BWM

Crystal Structure of Human Catechol O-Methyltransferase with bound SAM and DNC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H1Dpdb entry 1H1D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10.5293Tris, NaCl, MgCL2, DTT, CAPS, Na, K PO4, LiSO4, SAM, DNC, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0640.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.284α = 90
b = 66.648β = 90
c = 68.046γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2006-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.975076.80.085.411145111452
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.972.043.30.4482.32.31.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1H1D1.9833.31111101055954978.320.177040.174650.22514RANDOM26.975
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]
-1.61.170.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg15.114
r_dihedral_angle_3_deg13.331
r_dihedral_angle_1_deg5.152
r_scangle_it2.716
r_scbond_it1.626
r_angle_refined_deg1.269
r_mcangle_it1.119
r_angle_other_deg0.912
r_mcbond_it0.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg15.114
r_dihedral_angle_3_deg13.331
r_dihedral_angle_1_deg5.152
r_scangle_it2.716
r_scbond_it1.626
r_angle_refined_deg1.269
r_mcangle_it1.119
r_angle_other_deg0.912
r_mcbond_it0.581
r_symmetry_vdw_other0.257
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.128
r_mcbond_other0.103
r_symmetry_vdw_refined0.075
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1695
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing