5P93 | pdb_00005p93

humanized rat catechol O-methyltransferase in complex with single conformation of 5-(4-fluorophenyl)-2,3-dihydroxy-N-[2-(3-pyridin-4-yl-1H-1,2,4-triazol-5-yl)ethyl]benzamide at 1.24A

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
2.21	44.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.939	α = 90
b = 53.909	β = 90
c = 80.984	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		2010-02-01	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	1.24	44.88	98.6	0.054	0.057	0.999	25.58	9.24		61895		-3	16.237

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	1.24	1.27	86.4		0.267	0.289	0.964	7.72

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	1.24	44.88	57864	3066	96.98	0.115	0.1139	0.11	0.1351	0.13	RANDOM	11.823

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]
0.16			0.2		-0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.303
r_dihedral_angle_4_deg	17.435
r_rigid_bond_restr	14.793
r_sphericity_free	11.867
r_dihedral_angle_3_deg	11.827
r_sphericity_bonded	6.963
r_dihedral_angle_1_deg	5.085
r_angle_refined_deg	1.558
r_angle_other_deg	0.941
r_mcbond_it	0.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.303
r_dihedral_angle_4_deg	17.435
r_rigid_bond_restr	14.793
r_sphericity_free	11.867
r_dihedral_angle_3_deg	11.827
r_sphericity_bonded	6.963
r_dihedral_angle_1_deg	5.085
r_angle_refined_deg	1.558
r_angle_other_deg	0.941
r_mcbond_it	0.138
r_mcbond_other	0.107
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1673
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	65

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.