5P96 | pdb_00005p96

rat catechol O-methyltransferase in complex with N-[5-(2-aminopurin-9-yl)pentyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide at 1.40A

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	44.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.87	α = 90
b = 54.267	β = 90
c = 81.075	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	MARMOSAIC 225 mm CCD		2009-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.978200	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	1.4	36.72	99.7	0.048	0.052	0.999	23.75	6.88		43996		-3	17.578

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	1.4	1.44	97.1		0.251	0.274	0.963	6.49

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	1.4	36.72	40981	2199	97.99	0.1125	0.1107	0.11	0.1466	0.14	RANDOM	11.675

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]
0.07			0.21		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.441
r_dihedral_angle_4_deg	21.14
r_rigid_bond_restr	18.002
r_sphericity_free	13.203
r_dihedral_angle_3_deg	10.59
r_sphericity_bonded	6.704
r_dihedral_angle_1_deg	5.031
r_angle_refined_deg	1.777
r_angle_other_deg	1.044
r_mcbond_it	0.158

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.441
r_dihedral_angle_4_deg	21.14
r_rigid_bond_restr	18.002
r_sphericity_free	13.203
r_dihedral_angle_3_deg	10.59
r_sphericity_bonded	6.704
r_dihedral_angle_1_deg	5.031
r_angle_refined_deg	1.777
r_angle_other_deg	1.044
r_mcbond_it	0.158
r_mcbond_other	0.124
r_chiral_restr	0.105
r_bond_refined_d	0.016
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	1679
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	67

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.