Experiment: 4AND

CRYSTAL FORM II OF THE D93N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K44	PDB ENTRY 1K44

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		2.0 M AMMONIUM SULFATE, 2% (V/V) PEG400, 0.1 M HEPES, PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.419	α = 90
b = 108.419	β = 90
c = 108.419	γ = 90

Symmetry
Space Group	P 21 3

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		2006-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.81	26.3	99.9	0.08	23.6	11		10722		1	69.93

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	2.81	2.95	100		0.35	5.9	11.1

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 1K44	2.808	26.295	0.11	10557	502	99.29	0.2215	0.2199	0.2198	0.2516	0.2528	74.83

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.104
f_angle_d	0.765
f_chiral_restr	0.046
f_bond_d	0.003
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1958
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms

Software

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