2EXR | pdb_00002exr

X-Ray Structure of Cytokinin Oxidase/Dehydrogenase (CKX) From Arabidopsis Thaliana AT5G21482

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	Protein solution (10 mg/ml protein, 0.10 M Bis Tris, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, pH 7.0) mixed in a 1:1 ratio with the well solution (24% MEPEG 5K, 0.05 M magnesium sulfate, 0.1 M HEPPS pH 8.5),temperature 277K, vapor diffusion, hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.858	α = 90
b = 114.502	β = 90
c = 190.92	γ = 90

Symmetry
Space Group	C 2 2 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 300 mm CCD	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR	2005-10-10	M	MAD
2	1	x-ray		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97911, 0.96403	APS	22-ID

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	1.7	42.57	95.1	0.091	10.709	6.8		52961

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	1.7	1.76	73.4		0.232	4.373	4.8	4054

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	1.702	42.57	52917	2669	95.086	0.173	0.17331	0.1712	0.1818	0.2139	0.2202	RANDOM	26.484

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]
-0.098			1.633		-1.535

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.949
r_dihedral_angle_4_deg	13.478
r_dihedral_angle_3_deg	13.121
r_dihedral_angle_1_deg	5.608
r_scangle_it	4.643
r_scbond_it	3.331
r_mcangle_it	2.096
r_angle_refined_deg	1.392
r_mcbond_it	1.277
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.949
r_dihedral_angle_4_deg	13.478
r_dihedral_angle_3_deg	13.121
r_dihedral_angle_1_deg	5.608
r_scangle_it	4.643
r_scbond_it	3.331
r_mcangle_it	2.096
r_angle_refined_deg	1.392
r_mcbond_it	1.277
r_nbtor_refined	0.307
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3853
Nucleic Acid Atoms
Solvent Atoms	633
Heterogen Atoms	53

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
SHELXD	phasing
SOLOMON	phasing
ARP/wARP	model building

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.