Experiment: 4CET

Crystal structure of the complex of the P187S variant of human NAD(P) H:quinone oxidoreductase with dicoumarol at 2.2 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QBG	PDB ENTRY 1QBG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN WAS CRYSTALLIZED FROM 0.005 M CO(II)CL-HEXAHYDRATE, 0.005 M NI(II)CL-HEXAHYDRATE, 0.005 M CDCL-HYDRATE, 0.005 M MGCL-HEAXHYDRATE, 0.1 M HEPES PH 7.5, 12 % PEG-3350 (W/V)

Crystal Properties
Matthews coefficient	Solvent content
1.67	26.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.05	α = 90
b = 51.05	β = 90
c = 169.04	γ = 90

Symmetry
Space Group	P 41 21 2

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	DECTRIS PILATUS		2012-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R		ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	33.8	99.8	0.12	18.3	11.9		12127		3.2	26.84

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	98		0.66	3.2	9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1QBG	2.2	33.197	1.34	12065	576	99.77	0.178	0.1755	0.1756	0.2239	0.2223	34.2

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.626
f_angle_d	0.895
f_chiral_restr	0.06
f_bond_d	0.004
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1768
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	78

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing