2I1W | pdb_00002i1w

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	1U0R	PDB ENTRY 1U0R

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, 15-20% w/v polyethylene glycol 400, 10 mM KI, pH 5.4, VAPOR DIFFUSION, HANGING DROP, pH 5.40

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.612	α = 90
b = 119.017	β = 102.08
c = 67.937	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2004-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	2.34	34.37	97.5	0.066	13.9	3.5		42609		1

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	PDB ENTRY 1U0R	2.34	34.37	43681	41254	1330	97.49	0.19607	0.19408	0.22	0.25696	0.28	RANDOM	37.698

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]
-3.21		0.52	1.71		1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.277
r_dihedral_angle_4_deg	17.786
r_dihedral_angle_3_deg	17.126
r_dihedral_angle_1_deg	9.778
r_scangle_it	2.197
r_scbond_it	1.56
r_angle_refined_deg	1.374
r_angle_other_deg	0.934
r_mcangle_it	0.912
r_mcbond_it	0.636
r_symmetry_hbond_refined	0.615
r_symmetry_vdw_refined	0.34
r_xyhbond_nbd_refined	0.307
r_symmetry_vdw_other	0.264
r_nbd_other	0.205
r_nbd_refined	0.197
r_nbtor_refined	0.178
r_chiral_restr	0.132
r_mcbond_other	0.116
r_xyhbond_nbd_other	0.113
r_nbtor_other	0.086
r_bond_refined_d	0.013
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8157
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing