3PJ9 | pdb_00003pj9

Crystal structure of a Nucleoside Diphosphate Kinase from Campylobacter jejuni

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NCK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	2M NH4 Sulfate, 5% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.672	α = 90
b = 88.142	β = 90
c = 110.925	γ = 90

Symmetry
Space Group	P 21 21 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 225 mm CCD	MIRROR	2010-10-21	M	MOLECULAR REPLACEMENT

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	30	100	0.084	22.2	7.4	49704	49704		-3	40.3

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)
	2.1	2.14	100		0.57	3.6	7.5	2433

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2NCK	2.1	28.4	46976	46976	2511	99.15	0.17072	0.16956	0.1792	0.19199	0.2005	RANDOM	38.152

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]
0.71			0.94		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.515
r_dihedral_angle_4_deg	19.856
r_dihedral_angle_3_deg	14.42
r_dihedral_angle_1_deg	6.184
r_scangle_it	4.41
r_scbond_it	2.684
r_mcangle_it	1.557
r_angle_refined_deg	1.484
r_mcbond_it	0.854
r_chiral_restr	0.11
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4255
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	60

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CCP4	model building
MrBUMP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CCP4	phasing