2I29 | pdb_00002i29

Crystal structure of NAD kinase 1 from Listeria monocytogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I1W	PDB ENTRY 2I1W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4		0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.503	α = 90
b = 73.538	β = 90
c = 118.745	γ = 90

Symmetry
Space Group	I 2 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 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.979	ESRF	ID14-2

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	2.1	37.14	98.7	0.071	17.2	6	16111	15633			37.7

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2I1W	2.1	34.86	16111	15633	478	98.45	0.206	0.206	0.205	0.2067	0.254	0.2479	RANDOM	39.011

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]
0.68			3.79		-4.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.082
r_dihedral_angle_4_deg	19.956
r_dihedral_angle_3_deg	15.741
r_dihedral_angle_1_deg	9.342
r_angle_refined_deg	1.478
r_scangle_it	1.244
r_scbond_it	1.055
r_mcangle_it	0.707
r_mcbond_it	0.455
r_nbtor_refined	0.309
r_xyhbond_nbd_refined	0.299
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.17
r_chiral_restr	0.163
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1976
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing