3QWB | pdb_00003qwb

Crystal structure of Saccharomyces cerevisiae Zeta-crystallin-like quinone oxidoreductase Zta1 complexed with NADPH

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	25% polyethylene glycol 3350, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.961	α = 90
b = 75.362	β = 92.11
c = 182.833	γ = 90

Symmetry
Space Group	P 1 21 1

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		2009-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.979	SSRF	BL17U

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	1.59	50	97.2	0.106	8.67	3.5		190318

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	1.59	1.61	87.4		0.157	6.05	3.2	8502

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	PDB ENTRY 1QOR	1.59	35.5	180675	9637	97.31	0.18894	0.18774	0.1864	0.21133	0.21	RANDOM	16.774

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]
0.61			-0.2		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.712
r_dihedral_angle_4_deg	15.007
r_dihedral_angle_3_deg	12.326
r_dihedral_angle_1_deg	5.724
r_scangle_it	2.267
r_scbond_it	1.323
r_angle_refined_deg	1.28
r_mcangle_it	1.107
r_mcbond_it	0.67
r_chiral_restr	0.085
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10340
Nucleic Acid Atoms
Solvent Atoms	1627
Heterogen Atoms	222

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling