1ZX1 | pdb_00001zx1

Human quinone oxidoreductase 2 (NQO2) in complex with the cytostatic prodrug CB1954

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	Hepes, ammonium sulphate, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.328	α = 90
b = 84.341	β = 90
c = 106.579	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			2005-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.90010	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	50	97.4	0.128	11		29187	29187

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.18	82.8		0.411	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1QR2	2.16	50	25637	25637	1365	96.76	0.17591	0.17591	0.17418	0.18	0.20656	0.21	RANDOM	39.515

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]
-0.01			0.08		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.628
r_dihedral_angle_4_deg	25.192
r_dihedral_angle_3_deg	15.071
r_dihedral_angle_1_deg	6.122
r_scangle_it	3.357
r_scbond_it	2.093
r_angle_refined_deg	1.516
r_mcangle_it	1.279
r_mcbond_it	0.808
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.628
r_dihedral_angle_4_deg	25.192
r_dihedral_angle_3_deg	15.071
r_dihedral_angle_1_deg	6.122
r_scangle_it	3.357
r_scbond_it	2.093
r_angle_refined_deg	1.516
r_mcangle_it	1.279
r_mcbond_it	0.808
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.246
r_symmetry_hbond_refined	0.205
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.104
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_metal_ion_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3565
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	144

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.