5P94 | pdb_00005p94

humanized rat catechol O-methyltransferase in complex with 5-(4-fluorophenyl)-2,3-dihydroxy-N-[[3-[(1H-indazol-5-ylamino)methyl]phenyl]methyl]benzamide at 1.20A

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	44.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.967	α = 90
b = 54.237	β = 90
c = 80.648	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		2009-11-20	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	1.2	40.32	98.2	0.055	0.061	0.999	16.22	4.92		68073		-3	14.203

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	1.2	1.23	92.2		0.412	0.472	0.845	3.45

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	1.2	40.32	60319	3231	91.72	0.1311	0.1298	0.13	0.1568	0.15	RANDOM	9.933

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			0.06		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.229
r_rigid_bond_restr	16.927
r_dihedral_angle_4_deg	16.879
r_dihedral_angle_3_deg	12.553
r_sphericity_free	9.69
r_sphericity_bonded	5.269
r_dihedral_angle_1_deg	5.213
r_angle_refined_deg	1.754
r_angle_other_deg	0.937
r_chiral_restr	0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.229
r_rigid_bond_restr	16.927
r_dihedral_angle_4_deg	16.879
r_dihedral_angle_3_deg	12.553
r_sphericity_free	9.69
r_sphericity_bonded	5.269
r_dihedral_angle_1_deg	5.213
r_angle_refined_deg	1.754
r_angle_other_deg	0.937
r_chiral_restr	0.224
r_mcbond_it	0.124
r_mcbond_other	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1673
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	62

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.