5P92 | pdb_00005p92

humanized rat catechol O-methyltransferase in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-(4-thieno[2,3-c]pyridin-2-ylbutyl)benzamide at 1.61A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	AMMONIUM SULPHATE, CHES, PH 9

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.929	α = 90
b = 54.207	β = 90
c = 81.134	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	PIXEL	PSI PILATUS 6M		2010-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999900	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.61	45.07	98.8	0.052	0.057	0.999	21.93	6.19		28907		-3	21.344

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.65	86		0.134	0.155	0.975	6.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	1.61	45.07	27129	1445	97.38	0.1722	0.1704	0.18	0.2064	0.21	RANDOM	12.362

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]
0.13			0.44		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.465
r_dihedral_angle_4_deg	19.746
r_dihedral_angle_3_deg	12.579
r_dihedral_angle_1_deg	4.927
r_angle_refined_deg	1.825
r_angle_other_deg	1.57
r_chiral_restr	0.111
r_mcbond_it	0.03
r_mcbond_other	0.023
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.465
r_dihedral_angle_4_deg	19.746
r_dihedral_angle_3_deg	12.579
r_dihedral_angle_1_deg	4.927
r_angle_refined_deg	1.825
r_angle_other_deg	1.57
r_chiral_restr	0.111
r_mcbond_it	0.03
r_mcbond_other	0.023
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1673
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	60

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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 R01GM157729.