3A7E

Crystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VIDPDB ENTRY 1VID

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M Hepes pH7.5, 2% (v/v) PEG 400, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6253.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.909α = 90
b = 50.909β = 90
c = 168.186γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102003-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.54180SPring-8BL32B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.8281000.1630.1374.93.46717672738.4
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)
2.82.9599.90.3340.35212.73.5955

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1VID2.81058886541000.225580.217690.29819RANDOM38.503
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]
0.190.10.19-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.618
r_dihedral_angle_3_deg18.171
r_dihedral_angle_4_deg16.248
r_dihedral_angle_1_deg4.475
r_scangle_it3.184
r_scbond_it1.91
r_mcangle_it1.195
r_angle_refined_deg0.912
r_mcbond_it0.604
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.618
r_dihedral_angle_3_deg18.171
r_dihedral_angle_4_deg16.248
r_dihedral_angle_1_deg4.475
r_scangle_it3.184
r_scbond_it1.91
r_mcangle_it1.195
r_angle_refined_deg0.912
r_mcbond_it0.604
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1660
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms42

Software

Software
Software NamePurpose
BSSdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling