Experiment: 1VYA

Identification and characterization of the first plant G-quadruplex binding protein encoded by the Zea mays L. nucleoside diphosphate1 gene, ZmNDPK1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	100 mM sodium cacodylate (pH 6.5), 12% PEG 8000, and 200 mM CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.63	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.962	α = 90
b = 179.198	β = 99.28
c = 88.469	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	277	CCD	MARMOSAIC 225 mm CCD		2013-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	1.95	50	96.31	0.12	19.8	7.3		123697

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	1.95	1.98	92.3		0.66	1.75	4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1U8W	2.05	39.859	0.09	123697	1700	96.31	0.1609	0.1603	0.1576	0.2011	0.1977	Random selection	23.8

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]
2.9006		-2.9781	-0.9921		-1.9085

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.384
f_angle_d	1.013
f_chiral_restr	0.072
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14040
Nucleic Acid Atoms
Solvent Atoms	1663
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement