7CVW

Crystal structure of Catechol o-methyl transferase (COMT) from Niastella koreensis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	20% PEG4000, 20% 2-Propanol and 0.1M Sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.689	α = 90
b = 98.226	β = 90
c = 101.773	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	CCD	ADSC QUANTUM 270		2020-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.54	50	99.5	0.085	0.092	0.035	12.3	6.2		63757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57	99.1		0.313	0.35	0.153	0.826		4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	5N5D	1.54	27.55	60347	3366	99.41	0.175	0.1739	0.1951	RANDOM	13.533

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]
-0.63			0.21		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.062
r_dihedral_angle_4_deg	13.224
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	5.784
r_angle_refined_deg	2.663
r_angle_other_deg	1.709
r_chiral_restr	0.077
r_bond_other_d	0.042
r_bond_refined_d	0.029
r_gen_planes_refined	0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.062
r_dihedral_angle_4_deg	13.224
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	5.784
r_angle_refined_deg	2.663
r_angle_other_deg	1.709
r_chiral_restr	0.077
r_bond_other_d	0.042
r_bond_refined_d	0.029
r_gen_planes_refined	0.016
r_gen_planes_other	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3344
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	66

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.