3BWM

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H1D	pdb entry 1H1D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	293	Tris, NaCl, MgCL2, DTT, CAPS, Na, K PO4, LiSO4, SAM, DNC, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.23

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2006-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.97	50	76.8	0.08		5.4	11145	11145		2

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)	Redundancy	Number Unique Reflections (All)
	1.97	2.04	3.3		0.448	2.3	2.3	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1H1D	1.98	33.31	11110	10559	549	78.32	0.17704	0.17465	0.22514	RANDOM	26.975

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]
-1.6			1.17		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.825
r_dihedral_angle_4_deg	15.114
r_dihedral_angle_3_deg	13.331
r_dihedral_angle_1_deg	5.152
r_scangle_it	2.716
r_scbond_it	1.626
r_angle_refined_deg	1.269
r_mcangle_it	1.119
r_angle_other_deg	0.912
r_mcbond_it	0.581
r_symmetry_vdw_other	0.257
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.128
r_mcbond_other	0.103
r_symmetry_vdw_refined	0.075
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	1695
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing