Experiment: 3ZTR

Hexagonal form P6122 of the Aquifex aeolicus nucleoside diphosphate kinase (FIRST STAGE OF RADIATION DAMAGE)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZTO	PDB ENTRY 3ZTO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		25% PEG 3350, 0.2 M NACL, 0.1 M BIS-TRIS PH 5.5.

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 200.71	α = 90
b = 200.71	β = 90
c = 246.731	γ = 120

Symmetry
Space Group	P 61 2 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	CCD	ADSC QUANTUM 315r	KIRKPATRICK BAEZ	2008-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1		SOLEIL	PROXIMA 1

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	2.3	52.44	92	0.14	8	4.2		221854		1	18.39

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	2.3	2.42	93.4		0.35	3.6	4.2

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 3ZTO	2.3	52.444	0.49	221854	11149	89.82	0.1929	0.1915	0.1829	0.22	0.1835	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]
0.9956			0.9956		-1.9912

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.03
f_angle_d	1.214
f_chiral_restr	0.084
f_bond_d	0.012
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13380
Nucleic Acid Atoms
Solvent Atoms	1061
Heterogen Atoms

Software

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